.
|-- Readme.txt
|-- Readme_struts_version.txt
|-- cipres.txt
|-- eclipse.classpath
|-- eclipse.project
|-- eclipse.settings
|   |-- org.eclipse.jdt.core.prefs
|   |-- org.eclipse.jdt.ui.prefs
|   |-- org.eclipse.jst.common.project.facet.core.prefs
|   |-- org.eclipse.wst.common.component
|   |-- org.eclipse.wst.common.project.facet.core.xml
|   `-- org.eclipse.wst.validation.prefs
|-- pom.xml
|-- profiles.xml
|-- scripts
|   |-- release.sh
|   `-- tl.sh
|-- src
|   |-- main
|   |   |-- codeGeneration
|   |   |   |-- FreemarkerTemplate
|   |   |   |   |-- pise2JSP.ftl
|   |   |   |   |-- pise2JSPAdvanced.ftl
|   |   |   |   |-- pise2JSPSimple.ftl
|   |   |   |   |-- pise2JavaScript.ftl
|   |   |   |   |-- pise2JavaScriptControl.ftl
|   |   |   |   |-- pise2JavaScriptWarning.ftl
|   |   |   |   |-- pise2Logic.ftl
|   |   |   |   |-- pise2action.ftl
|   |   |   |   |-- pise2action_defaultValues.ftl
|   |   |   |   |-- pise2action_old.ftl
|   |   |   |   |-- pise2help.ftl
|   |   |   |   |-- pise2outputProperties.ftl
|   |   |   |   |-- pise2property.ftl
|   |   |   |   |-- pise2registry.ftl
|   |   |   |   |-- pise2strutsXML.ftl
|   |   |   |   |-- pise2validationJava.ftl
|   |   |   |   |-- pise2validationXML_old.ftl
|   |   |   |   |-- pise2valueDefaultTest.ftl
|   |   |   |   |-- pise2valueDefaultTestInfile.ftl
|   |   |   |   |-- pisePrecondExtract.ftl
|   |   |   |   `-- tool_registry2list.ftl
|   |   |   |-- Pise_5.a_latest
|   |   |   |   |-- CSR.xml
|   |   |   |   |-- PARSER
|   |   |   |   |   |-- README
|   |   |   |   |   |-- pise.dtd
|   |   |   |   |   `-- pise.xsd
|   |   |   |   |-- Puzzle.xml
|   |   |   |   |-- RepeatMasker.xml
|   |   |   |   |-- XMLDIR
|   |   |   |   |   |-- blast_init.xml
|   |   |   |   |   |-- emboss.xml
|   |   |   |   |   |-- fastapath.xml
|   |   |   |   |   |-- genewisepar_param.xml
|   |   |   |   |   |-- glimmer_header.xml
|   |   |   |   |   |-- hmmpar_param.xml
|   |   |   |   |   |-- nucdbs.xml
|   |   |   |   |   |-- phylip_header.xml
|   |   |   |   |   `-- protdbs.xml
|   |   |   |   |-- aaindexextract.xml
|   |   |   |   |-- abiview.xml
|   |   |   |   |-- aconvert.xml
|   |   |   |   |-- addquart.xml
|   |   |   |   |-- align2model.xml
|   |   |   |   |-- alignfit.xml
|   |   |   |   |-- alistat.xml
|   |   |   |   |-- amps.xml
|   |   |   |   |-- antigenic.xml
|   |   |   |   |-- assp.xml
|   |   |   |   |-- avestruc.xml
|   |   |   |   |-- backtranseq.xml
|   |   |   |   |-- bambe.xml
|   |   |   |   |-- banana.xml
|   |   |   |   |-- bionj.xml
|   |   |   |   |-- biosed.xml
|   |   |   |   |-- bl2seq.xml
|   |   |   |   |-- blast2.xml
|   |   |   |   |-- blast_init.xml
|   |   |   |   |-- blastpar.xml
|   |   |   |   |-- blastz.xml
|   |   |   |   |-- blimps.xml
|   |   |   |   |-- blimps_block.xml
|   |   |   |   |-- blimps_matrix.xml
|   |   |   |   |-- boxshade.xml
|   |   |   |   |-- btwisted.xml
|   |   |   |   |-- build_icm.xml
|   |   |   |   |-- buildmodel.xml
|   |   |   |   |-- cai.xml
|   |   |   |   |-- cap3.xml
|   |   |   |   |-- cds.xml
|   |   |   |   |-- chaos.xml
|   |   |   |   |-- charge.xml
|   |   |   |   |-- checktrans.xml
|   |   |   |   |-- chips.xml
|   |   |   |   |-- cirdna.xml
|   |   |   |   |-- clique.xml
|   |   |   |   |-- clustalw.xml
|   |   |   |   |-- clustalw_convert.xml
|   |   |   |   |-- clustalwpar.xml
|   |   |   |   |-- codcmp.xml
|   |   |   |   |-- coderet.xml
|   |   |   |   |-- codnocod.xml
|   |   |   |   |-- codontree.xml
|   |   |   |   |-- codonw.xml
|   |   |   |   |-- coils2.xml
|   |   |   |   |-- comalign.xml
|   |   |   |   |-- combat.xml
|   |   |   |   |-- complex.xml
|   |   |   |   |-- compseq.xml
|   |   |   |   |-- con_filter.xml
|   |   |   |   |-- confmat.xml
|   |   |   |   |-- cons.xml
|   |   |   |   |-- consense.xml
|   |   |   |   |-- consensus.xml
|   |   |   |   |-- corbatest.xml
|   |   |   |   |-- cosa.xml
|   |   |   |   |-- cpgplot.xml
|   |   |   |   |-- cpgreport.xml
|   |   |   |   |-- cusp.xml
|   |   |   |   |-- cutseq.xml
|   |   |   |   |-- dan.xml
|   |   |   |   |-- dca.xml
|   |   |   |   |-- decorate.xml
|   |   |   |   |-- degapseq.xml
|   |   |   |   |-- demoalign.xml
|   |   |   |   |-- demoreport.xml
|   |   |   |   |-- descseq.xml
|   |   |   |   |-- dialign2.xml
|   |   |   |   |-- dichet.xml
|   |   |   |   |-- diffseq.xml
|   |   |   |   |-- digest.xml
|   |   |   |   |-- distmat.xml
|   |   |   |   |-- distquart.xml
|   |   |   |   |-- dnadist.xml
|   |   |   |   |-- dnapars.xml
|   |   |   |   |-- dollop.xml
|   |   |   |   |-- domainer.xml
|   |   |   |   |-- dotmatcher.xml
|   |   |   |   |-- dotpath.xml
|   |   |   |   |-- dottup.xml
|   |   |   |   |-- drawgram.xml
|   |   |   |   |-- drawpyr.xml
|   |   |   |   |-- drawtree.xml
|   |   |   |   |-- dreg.xml
|   |   |   |   |-- druid.xml
|   |   |   |   |-- dsc.xml
|   |   |   |   |-- dssp.xml
|   |   |   |   |-- dstamp.xml
|   |   |   |   |-- echo.xml
|   |   |   |   |-- einverted.xml
|   |   |   |   |-- emboss.xml
|   |   |   |   |-- embossversion.xml
|   |   |   |   |-- emma.xml
|   |   |   |   |-- emowse.xml
|   |   |   |   |-- entret.xml
|   |   |   |   |-- environ.xml
|   |   |   |   |-- epestfind.xml
|   |   |   |   |-- eprimer3.xml
|   |   |   |   |-- equicktandem.xml
|   |   |   |   |-- est2genome.xml
|   |   |   |   |-- etandem.xml
|   |   |   |   |-- extractcds.xml
|   |   |   |   |-- extractfeat.xml
|   |   |   |   |-- extractseq.xml
|   |   |   |   |-- fasta.xml
|   |   |   |   |-- fastapath.xml
|   |   |   |   |-- fastasplitter.xml
|   |   |   |   |-- fastdnaml.xml
|   |   |   |   |-- fastdnamlpar.xml
|   |   |   |   |-- fastrna.xml
|   |   |   |   |-- filtersites.xml
|   |   |   |   |-- findkm.xml
|   |   |   |   |-- fitch.xml
|   |   |   |   |-- fmtseq.xml
|   |   |   |   |-- freak.xml
|   |   |   |   |-- full_run.xml
|   |   |   |   |-- funky.xml
|   |   |   |   |-- fuzznuc.xml
|   |   |   |   |-- fuzzpro.xml
|   |   |   |   |-- fuzztran.xml
|   |   |   |   |-- garnier.xml
|   |   |   |   |-- gb2xml.xml
|   |   |   |   |-- geecee.xml
|   |   |   |   |-- genemark.xml
|   |   |   |   |-- genewisepar_param.xml
|   |   |   |   |-- genewiseprotpar.xml
|   |   |   |   |-- genscan.xml
|   |   |   |   |-- getblock.xml
|   |   |   |   |-- getorf.xml
|   |   |   |   |-- gff2pf.xml
|   |   |   |   |-- gff2ps.xml
|   |   |   |   |-- gibbs.xml
|   |   |   |   |-- gibbs_scan.xml
|   |   |   |   |-- glimmer.xml
|   |   |   |   |-- glimmer_extract.xml
|   |   |   |   |-- glimmer_header.xml
|   |   |   |   |-- golden.xml
|   |   |   |   |-- grailclnt.xml
|   |   |   |   |-- gruppi.xml
|   |   |   |   |-- helixturnhelix.xml
|   |   |   |   |-- hmmalign.xml
|   |   |   |   |-- hmmbuild.xml
|   |   |   |   |-- hmmcalibrate.xml
|   |   |   |   |-- hmmconvert.xml
|   |   |   |   |-- hmmemit.xml
|   |   |   |   |-- hmmer2sam.xml
|   |   |   |   |-- hmmfetch.xml
|   |   |   |   |-- hmmpar.xml
|   |   |   |   |-- hmmpar_param.xml
|   |   |   |   |-- hmmparhmmscore.xml
|   |   |   |   |-- hmmpfam.xml
|   |   |   |   |-- hmmpfampar.xml
|   |   |   |   |-- hmmscore.xml
|   |   |   |   |-- hmmsearch.xml
|   |   |   |   |-- hmmsearchpar.xml
|   |   |   |   |-- hmoment.xml
|   |   |   |   |-- homology.xml
|   |   |   |   |-- html4blast.xml
|   |   |   |   |-- iep.xml
|   |   |   |   |-- infoalign.xml
|   |   |   |   |-- infoseq.xml
|   |   |   |   |-- intconv.xml
|   |   |   |   |-- interface.xml
|   |   |   |   |-- isochore.xml
|   |   |   |   |-- kitsch.xml
|   |   |   |   |-- lassap.xml
|   |   |   |   |-- lgicsearch.xml
|   |   |   |   |-- lib
|   |   |   |   |   |-- Pise-5.a-xml.tar.gz
|   |   |   |   |   `-- Pise-5.a.tar.gz
|   |   |   |   |-- lindna.xml
|   |   |   |   |-- listor.xml
|   |   |   |   |-- loadseq.xml
|   |   |   |   |-- long_orfs.xml
|   |   |   |   |-- lspcalc_prosite.xml
|   |   |   |   |-- lspcalc_seqdb.xml
|   |   |   |   |-- lspcalc_seqseq.xml
|   |   |   |   |-- lspread_prosite.xml
|   |   |   |   |-- lspread_seqdb.xml
|   |   |   |   |-- lspread_seqseq.xml
|   |   |   |   |-- lvb.xml
|   |   |   |   |-- makehist.xml
|   |   |   |   |-- map.xml
|   |   |   |   |-- marscan.xml
|   |   |   |   |-- maskfeat.xml
|   |   |   |   |-- maskseq.xml
|   |   |   |   |-- matcher.xml
|   |   |   |   |-- megablastpar.xml
|   |   |   |   |-- megamerger.xml
|   |   |   |   |-- melting.xml
|   |   |   |   |-- merger.xml
|   |   |   |   |-- mfold.xml
|   |   |   |   |-- mix.xml
|   |   |   |   |-- mmsearch.xml
|   |   |   |   |-- modelfromalign.xml
|   |   |   |   |-- morgan.xml
|   |   |   |   |-- most.xml
|   |   |   |   |-- mreps.xml
|   |   |   |   |-- msa.xml
|   |   |   |   |-- msbar.xml
|   |   |   |   |-- mspcrunch.xml
|   |   |   |   |-- mview_alig.xml
|   |   |   |   |-- mview_blast.xml
|   |   |   |   |-- mwfilter.xml
|   |   |   |   |-- needle.xml
|   |   |   |   |-- neighbor.xml
|   |   |   |   |-- newcoils.xml
|   |   |   |   |-- newcpgreport.xml
|   |   |   |   |-- newcpgseek.xml
|   |   |   |   |-- newseq.xml
|   |   |   |   |-- njdist.xml
|   |   |   |   |-- nnssp.xml
|   |   |   |   |-- notseq.xml
|   |   |   |   |-- nrscope.xml
|   |   |   |   |-- nthseq.xml
|   |   |   |   |-- nucdbs.xml
|   |   |   |   |-- octanol.xml
|   |   |   |   |-- oddcomp.xml
|   |   |   |   |-- palindrome.xml
|   |   |   |   |-- pam.xml
|   |   |   |   |-- parciquart.xml
|   |   |   |   |-- pars.xml
|   |   |   |   |-- pasteseq.xml
|   |   |   |   |-- path.xml
|   |   |   |   |-- patmatdb.xml
|   |   |   |   |-- patmatmotifs.xml
|   |   |   |   |-- patmattest.xml
|   |   |   |   |-- patser.xml
|   |   |   |   |-- pdbc.xml
|   |   |   |   |-- pdbsearch.xml
|   |   |   |   |-- pdbseq.xml
|   |   |   |   |-- pdbtosp.xml
|   |   |   |   |-- pepcoil.xml
|   |   |   |   |-- pepinfo.xml
|   |   |   |   |-- pepnet.xml
|   |   |   |   |-- pepstats.xml
|   |   |   |   |-- pepwheel.xml
|   |   |   |   |-- pepwindow.xml
|   |   |   |   |-- pepwindowall.xml
|   |   |   |   |-- pestfind.xml
|   |   |   |   |-- pftools.xml
|   |   |   |   |-- phiblast.xml
|   |   |   |   |-- phylip_header.xml
|   |   |   |   |-- phyml.xml
|   |   |   |   |-- pima.xml
|   |   |   |   |-- plotcon.xml
|   |   |   |   |-- plotorf.xml
|   |   |   |   |-- plsearch.xml
|   |   |   |   |-- polydot.xml
|   |   |   |   |-- pratt.xml
|   |   |   |   |-- predator.xml
|   |   |   |   |-- preg.xml
|   |   |   |   |-- prettyalign.xml
|   |   |   |   |-- prettyplot.xml
|   |   |   |   |-- prettyseq.xml
|   |   |   |   |-- prima.xml
|   |   |   |   |-- primers.xml
|   |   |   |   |-- primersearch.xml
|   |   |   |   |-- primo.xml
|   |   |   |   |-- primo.xml.xml
|   |   |   |   |-- prodom.xml
|   |   |   |   |-- profit.xml
|   |   |   |   |-- prophecy.xml
|   |   |   |   |-- prophet.xml
|   |   |   |   |-- prose.xml
|   |   |   |   |-- prosearch.xml
|   |   |   |   |-- prot_nucml.xml
|   |   |   |   |-- protal2dna.xml
|   |   |   |   |-- protdbs.xml
|   |   |   |   |-- protdist.xml
|   |   |   |   |-- protnuc_ml.xml
|   |   |   |   |-- protpars.xml
|   |   |   |   |-- pscan.xml
|   |   |   |   |-- psiblast.xml
|   |   |   |   |-- psiblastpar.xml
|   |   |   |   |-- psort2.xml
|   |   |   |   |-- pyramids.xml
|   |   |   |   |-- pyreval.xml
|   |   |   |   |-- qatest.xml
|   |   |   |   |-- qstar.xml
|   |   |   |   |-- quicktree.xml
|   |   |   |   |-- readnexus.xml
|   |   |   |   |-- readseq.xml
|   |   |   |   |-- recoder.xml
|   |   |   |   |-- redata.xml
|   |   |   |   |-- remap.xml
|   |   |   |   |-- repeats.xml
|   |   |   |   |-- reputer.xml
|   |   |   |   |-- restover.xml
|   |   |   |   |-- restrict.xml
|   |   |   |   |-- revseq.xml
|   |   |   |   |-- rif.xml
|   |   |   |   |-- rnadistance.xml
|   |   |   |   |-- rnaeval.xml
|   |   |   |   |-- rnafold.xml
|   |   |   |   |-- rnaga.xml
|   |   |   |   |-- rnaheat.xml
|   |   |   |   |-- rnainverse.xml
|   |   |   |   |-- rnapdist.xml
|   |   |   |   |-- rnasubopt.xml
|   |   |   |   |-- sam2hmmer.xml
|   |   |   |   |-- sampleseqs.xml
|   |   |   |   |-- saps.xml
|   |   |   |   |-- satellites.xml
|   |   |   |   |-- scan_for_matches.xml
|   |   |   |   |-- scope.xml
|   |   |   |   |-- scopparse.xml
|   |   |   |   |-- screen2h.xml
|   |   |   |   |-- seqboot.xml
|   |   |   |   |-- seqclean.xml
|   |   |   |   |-- seqgen.xml
|   |   |   |   |-- seqinfo.xml
|   |   |   |   |-- seqmatchall.xml
|   |   |   |   |-- seqret.xml
|   |   |   |   |-- seqretall.xml
|   |   |   |   |-- seqretallfeat.xml
|   |   |   |   |-- seqretset.xml
|   |   |   |   |-- seqretsingle.xml
|   |   |   |   |-- seqsblast.xml
|   |   |   |   |-- seqstat.xml
|   |   |   |   |-- showalign.xml
|   |   |   |   |-- showdb.xml
|   |   |   |   |-- showfeat.xml
|   |   |   |   |-- showorf.xml
|   |   |   |   |-- showseq.xml
|   |   |   |   |-- shuffleseq.xml
|   |   |   |   |-- sig.xml
|   |   |   |   |-- sigcleave.xml
|   |   |   |   |-- siggen.xml
|   |   |   |   |-- sigplot.xml
|   |   |   |   |-- sigscan.xml
|   |   |   |   |-- silent.xml
|   |   |   |   |-- sirna.xml
|   |   |   |   |-- sixpack.xml
|   |   |   |   |-- skipseq.xml
|   |   |   |   |-- smile.xml
|   |   |   |   |-- smile2.xml
|   |   |   |   |-- sorttrans.xml
|   |   |   |   |-- spacne.xml
|   |   |   |   |-- splitter.xml
|   |   |   |   |-- sputnik.xml
|   |   |   |   |-- squizz.xml
|   |   |   |   |-- sreformat.xml
|   |   |   |   |-- ssearch.xml
|   |   |   |   |-- stamp.xml
|   |   |   |   |-- stamps.xml
|   |   |   |   |-- stretcher.xml
|   |   |   |   |-- stride.xml
|   |   |   |   |-- stssearch.xml
|   |   |   |   |-- supermatcher.xml
|   |   |   |   |-- swissparse.xml
|   |   |   |   |-- syco.xml
|   |   |   |   |-- t_coffee.xml
|   |   |   |   |-- tacg.xml
|   |   |   |   |-- tcode.xml
|   |   |   |   |-- tfscan.xml
|   |   |   |   |-- tipdate.xml
|   |   |   |   |-- titi.xml
|   |   |   |   |-- tmap.xml
|   |   |   |   |-- toppred.xml
|   |   |   |   |-- tranalign.xml
|   |   |   |   |-- transeq.xml
|   |   |   |   |-- transform.xml
|   |   |   |   |-- treealign.xml
|   |   |   |   |-- treetypedisplay.xml
|   |   |   |   |-- trimest.xml
|   |   |   |   |-- trimseq.xml
|   |   |   |   |-- trnascan.xml
|   |   |   |   |-- twofeat.xml
|   |   |   |   |-- union.xml
|   |   |   |   |-- unroot.xml
|   |   |   |   |-- vectorstrip.xml
|   |   |   |   |-- water.xml
|   |   |   |   |-- weighbor.xml
|   |   |   |   |-- whichdb.xml
|   |   |   |   |-- wise.xml
|   |   |   |   |-- wise2.xml
|   |   |   |   |-- wobble.xml
|   |   |   |   |-- wordcount.xml
|   |   |   |   |-- wordmatch.xml
|   |   |   |   |-- wublast2.xml
|   |   |   |   |-- xblast.xml
|   |   |   |   |-- xpound.xml
|   |   |   |   `-- yank.xml
|   |   |   |-- README
|   |   |   |-- build.xml
|   |   |   `-- lib
|   |   |       |-- jar
|   |   |       |   |-- freemarker-2.3.8.jar
|   |   |       |   `-- xmltask-v1.14.jar
|   |   |       `-- struts-tools.xml
|   |   |-- docs
|   |   |   `-- build-deploy.txt
|   |   |-- java
|   |   |   `-- org
|   |   |       `-- ngbw
|   |   |           `-- web
|   |   |               |-- actions
|   |   |               |   |-- ArchiveManager.java
|   |   |               |   |-- CreateData.java
|   |   |               |   |-- CreateTask.java
|   |   |               |   |-- DataManager.java
|   |   |               |   |-- DownloadAction.java
|   |   |               |   |-- FolderManager.java
|   |   |               |   |-- ManageTasks.java
|   |   |               |   |-- NgbwSupport.java
|   |   |               |   |-- ProfileManager.java
|   |   |               |   |-- RegisterStatistics.java
|   |   |               |   |-- RegisterUser.java
|   |   |               |   |-- SearchData.java
|   |   |               |   |-- SessionManager.java
|   |   |               |   |-- SetTaskOutput.java
|   |   |               |   |-- TaskUpdate.java
|   |   |               |   |-- ToolParameters.java
|   |   |               |   |-- ajax
|   |   |               |   |   |-- DataUploadLists.java
|   |   |               |   |   |-- DatasetLists.java
|   |   |               |   |   `-- ToggleFolder.java
|   |   |               |   `-- tool
|   |   |               |       |-- align.java
|   |   |               |       |-- beast_tg.java
|   |   |               |       |-- bl2seq.java
|   |   |               |       |-- blast2.java
|   |   |               |       |-- blastn.java
|   |   |               |       |-- blastp.java
|   |   |               |       |-- blastx.java
|   |   |               |       |-- blimps.java
|   |   |               |       |-- boxshade.java
|   |   |               |       |-- bucky.java
|   |   |               |       |-- clearcut.java
|   |   |               |       |-- clique.java
|   |   |               |       |-- clustalw.java
|   |   |               |       |-- clustalw_dist.java
|   |   |               |       |-- clustalw_n.java
|   |   |               |       |-- clustalw_p.java
|   |   |               |       |-- clustalw_profile.java
|   |   |               |       |-- clustalw_tree.java
|   |   |               |       |-- compass.java
|   |   |               |       |-- consense.java
|   |   |               |       |-- contralign.java
|   |   |               |       |-- degapseq.java
|   |   |               |       |-- dnadist.java
|   |   |               |       |-- dnapars.java
|   |   |               |       |-- dollop.java
|   |   |               |       |-- drawgram.java
|   |   |               |       |-- drawtree.java
|   |   |               |       |-- dssp.java
|   |   |               |       |-- epestfind.java
|   |   |               |       |-- eprimer3.java
|   |   |               |       |-- extractalign.java
|   |   |               |       |-- extractseq.java
|   |   |               |       |-- fasta_n.java
|   |   |               |       |-- fasta_p.java
|   |   |               |       |-- fastx.java
|   |   |               |       |-- fasty.java
|   |   |               |       |-- fingerprintscan.java
|   |   |               |       |-- fitch.java
|   |   |               |       |-- formatvalidator.java
|   |   |               |       |-- fsa.java
|   |   |               |       |-- garli.java
|   |   |               |       |-- garli2_tgb.java
|   |   |               |       |-- garli_abe.java
|   |   |               |       |-- garli_conf_creator.java
|   |   |               |       |-- garli_lonestar.java
|   |   |               |       |-- garli_tg.java
|   |   |               |       |-- helixturnhelix.java
|   |   |               |       |-- hmmpfam.java
|   |   |               |       |-- kitsch.java
|   |   |               |       |-- lalign.java
|   |   |               |       |-- mafft.java
|   |   |               |       |-- mafft_tg.java
|   |   |               |       |-- mafftnew.java
|   |   |               |       |-- mbsum.java
|   |   |               |       |-- merger.java
|   |   |               |       |-- mfold.java
|   |   |               |       |-- mix.java
|   |   |               |       |-- mrbayes.java
|   |   |               |       |-- mrbayes_abe.java
|   |   |               |       |-- mrbayes_lonestar.java
|   |   |               |       |-- mrbayeshybrid_abe.java
|   |   |               |       |-- mrbayeshybrid_tg.java
|   |   |               |       |-- msa.java
|   |   |               |       |-- muscle.java
|   |   |               |       |-- mview_alig.java
|   |   |               |       |-- mview_blast.java
|   |   |               |       |-- nclconverter.java
|   |   |               |       |-- neighbor.java
|   |   |               |       |-- new_tool.java
|   |   |               |       |-- pars.java
|   |   |               |       |-- paup.java
|   |   |               |       |-- pauprat.java
|   |   |               |       |-- pauprat_exp.java
|   |   |               |       |-- pepinfo.java
|   |   |               |       |-- pepstats.java
|   |   |               |       |-- pepwindow.java
|   |   |               |       |-- pfscan.java
|   |   |               |       |-- pfsearch.java
|   |   |               |       |-- phyml.java
|   |   |               |       |-- poy.java
|   |   |               |       |-- poy2.java
|   |   |               |       |-- ppsearch.java
|   |   |               |       |-- probalign.java
|   |   |               |       |-- probcons.java
|   |   |               |       |-- prosearch.java
|   |   |               |       |-- protdist.java
|   |   |               |       |-- proteus.java
|   |   |               |       |-- protpars.java
|   |   |               |       |-- prss.java
|   |   |               |       |-- psiblast.java
|   |   |               |       |-- psipred.java
|   |   |               |       |-- raxmlhpc.java
|   |   |               |       |-- raxmlhpc2.java
|   |   |               |       |-- raxmlhpc2_abe.java
|   |   |               |       |-- raxmlhpc2_abe727.java
|   |   |               |       |-- raxmlhpc2_abe_727.java
|   |   |               |       |-- raxmlhpc2_tg.java
|   |   |               |       |-- raxmlhpc2_tgb.java
|   |   |               |       |-- raxmlhpc2bb.java
|   |   |               |       |-- raxmlhpc_abe.java
|   |   |               |       |-- readseq.java
|   |   |               |       |-- restrict.java
|   |   |               |       |-- revseq.java
|   |   |               |       |-- rid3paup.java
|   |   |               |       |-- rid3raxml.java
|   |   |               |       |-- rpsblast.java
|   |   |               |       |-- saps.java
|   |   |               |       |-- seqboot.java
|   |   |               |       |-- seqretsplit.java
|   |   |               |       |-- sixpack.java
|   |   |               |       |-- sleep.java
|   |   |               |       |-- spidey.java
|   |   |               |       |-- ssearch_n.java
|   |   |               |       |-- ssearch_p.java
|   |   |               |       |-- tacg.java
|   |   |               |       |-- tblastn.java
|   |   |               |       |-- tblastx.java
|   |   |               |       |-- tfasta.java
|   |   |               |       |-- tfastx.java
|   |   |               |       |-- tfasty.java
|   |   |               |       |-- tmap.java
|   |   |               |       `-- unroot.java
|   |   |               |-- controllers
|   |   |               |   |-- DataController.java
|   |   |               |   |-- DataFormatController.java
|   |   |               |   |-- DatasetController.java
|   |   |               |   |-- FolderController.java
|   |   |               |   |-- RecordTypeController.java
|   |   |               |   `-- SessionController.java
|   |   |               |-- interceptors
|   |   |               |   |-- AuthenticationInterceptor.java
|   |   |               |   |-- NavigationInterceptor.java
|   |   |               |   `-- SessionListener.java
|   |   |               |-- model
|   |   |               |   |-- Page.java
|   |   |               |   |-- Tab.java
|   |   |               |   |-- TabbedPanel.java
|   |   |               |   `-- impl
|   |   |               |       |-- ConceptComparator.java
|   |   |               |       |-- DataRecordPage.java
|   |   |               |       |-- ListPage.java
|   |   |               |       |-- RecordFieldTypeComparator.java
|   |   |               |       |-- ToolComparator.java
|   |   |               |       `-- tool
|   |   |               |           |-- alignValidator.java
|   |   |               |           |-- beast_tgValidator.java
|   |   |               |           |-- bl2seqValidator.java
|   |   |               |           |-- blast2Validator.java
|   |   |               |           |-- blastnValidator.java
|   |   |               |           |-- blastpValidator.java
|   |   |               |           |-- blastxValidator.java
|   |   |               |           |-- blimpsValidator.java
|   |   |               |           |-- boxshadeValidator.java
|   |   |               |           |-- buckyValidator.java
|   |   |               |           |-- clearcutValidator.java
|   |   |               |           |-- cliqueValidator.java
|   |   |               |           |-- clustalwValidator.java
|   |   |               |           |-- clustalw_distValidator.java
|   |   |               |           |-- clustalw_nValidator.java
|   |   |               |           |-- clustalw_pValidator.java
|   |   |               |           |-- clustalw_profileValidator.java
|   |   |               |           |-- clustalw_treeValidator.java
|   |   |               |           |-- compassValidator.java
|   |   |               |           |-- consenseValidator.java
|   |   |               |           |-- contralignValidator.java
|   |   |               |           |-- degapseqValidator.java
|   |   |               |           |-- dnadistValidator.java
|   |   |               |           |-- dnaparsValidator.java
|   |   |               |           |-- dollopValidator.java
|   |   |               |           |-- drawgramValidator.java
|   |   |               |           |-- drawtreeValidator.java
|   |   |               |           |-- dsspValidator.java
|   |   |               |           |-- epestfindValidator.java
|   |   |               |           |-- eprimer3Validator.java
|   |   |               |           |-- extractalignValidator.java
|   |   |               |           |-- extractseqValidator.java
|   |   |               |           |-- fasta_nValidator.java
|   |   |               |           |-- fasta_pValidator.java
|   |   |               |           |-- fastxValidator.java
|   |   |               |           |-- fastyValidator.java
|   |   |               |           |-- fingerprintscanValidator.java
|   |   |               |           |-- fitchValidator.java
|   |   |               |           |-- formatvalidatorValidator.java
|   |   |               |           |-- fsaValidator.java
|   |   |               |           |-- garli2_tgbValidator.java
|   |   |               |           |-- garliValidator.java
|   |   |               |           |-- garli_abeValidator.java
|   |   |               |           |-- garli_conf_creatorValidator.java
|   |   |               |           |-- garli_lonestarValidator.java
|   |   |               |           |-- garli_tgValidator.java
|   |   |               |           |-- helixturnhelixValidator.java
|   |   |               |           |-- hmmpfamValidator.java
|   |   |               |           |-- kitschValidator.java
|   |   |               |           |-- lalignValidator.java
|   |   |               |           |-- mafftValidator.java
|   |   |               |           |-- mafft_tgValidator.java
|   |   |               |           |-- mafftnewValidator.java
|   |   |               |           |-- mbsumValidator.java
|   |   |               |           |-- mergerValidator.java
|   |   |               |           |-- mfoldValidator.java
|   |   |               |           |-- mixValidator.java
|   |   |               |           |-- mrbayesValidator.java
|   |   |               |           |-- mrbayes_abeValidator.java
|   |   |               |           |-- mrbayes_lonestarValidator.java
|   |   |               |           |-- mrbayeshybrid_abeValidator.java
|   |   |               |           |-- mrbayeshybrid_tgValidator.java
|   |   |               |           |-- msaValidator.java
|   |   |               |           |-- muscleValidator.java
|   |   |               |           |-- mview_aligValidator.java
|   |   |               |           |-- mview_blastValidator.java
|   |   |               |           |-- nclconverterValidator.java
|   |   |               |           |-- neighborValidator.java
|   |   |               |           |-- new_toolValidator.java
|   |   |               |           |-- parsValidator.java
|   |   |               |           |-- paupValidator.java
|   |   |               |           |-- paupratValidator.java
|   |   |               |           |-- pauprat_expValidator.java
|   |   |               |           |-- pepinfoValidator.java
|   |   |               |           |-- pepstatsValidator.java
|   |   |               |           |-- pepwindowValidator.java
|   |   |               |           |-- pfscanValidator.java
|   |   |               |           |-- pfsearchValidator.java
|   |   |               |           |-- phymlValidator.java
|   |   |               |           |-- poy2Validator.java
|   |   |               |           |-- poyValidator.java
|   |   |               |           |-- ppsearchValidator.java
|   |   |               |           |-- probalignValidator.java
|   |   |               |           |-- probconsValidator.java
|   |   |               |           |-- prosearchValidator.java
|   |   |               |           |-- protdistValidator.java
|   |   |               |           |-- proteusValidator.java
|   |   |               |           |-- protparsValidator.java
|   |   |               |           |-- prssValidator.java
|   |   |               |           |-- psiblastValidator.java
|   |   |               |           |-- psipredValidator.java
|   |   |               |           |-- raxmlhpc2Validator.java
|   |   |               |           |-- raxmlhpc2_abe727Validator.java
|   |   |               |           |-- raxmlhpc2_abeValidator.java
|   |   |               |           |-- raxmlhpc2_abe_727Validator.java
|   |   |               |           |-- raxmlhpc2_tgValidator.java
|   |   |               |           |-- raxmlhpc2_tgbValidator.java
|   |   |               |           |-- raxmlhpc2bbValidator.java
|   |   |               |           |-- raxmlhpcValidator.java
|   |   |               |           |-- raxmlhpc_abeValidator.java
|   |   |               |           |-- readseqValidator.java
|   |   |               |           |-- restrictValidator.java
|   |   |               |           |-- revseqValidator.java
|   |   |               |           |-- rid3paupValidator.java
|   |   |               |           |-- rid3raxmlValidator.java
|   |   |               |           |-- rpsblastValidator.java
|   |   |               |           |-- sapsValidator.java
|   |   |               |           |-- seqbootValidator.java
|   |   |               |           |-- seqretsplitValidator.java
|   |   |               |           |-- sixpackValidator.java
|   |   |               |           |-- sleepValidator.java
|   |   |               |           |-- spideyValidator.java
|   |   |               |           |-- ssearch_nValidator.java
|   |   |               |           |-- ssearch_pValidator.java
|   |   |               |           |-- tacgValidator.java
|   |   |               |           |-- tblastnValidator.java
|   |   |               |           |-- tblastxValidator.java
|   |   |               |           |-- tfastaValidator.java
|   |   |               |           |-- tfastxValidator.java
|   |   |               |           |-- tfastyValidator.java
|   |   |               |           |-- tmapValidator.java
|   |   |               |           `-- unrootValidator.java
|   |   |               `-- treeimage
|   |   |                   |-- DownloadAction.java
|   |   |                   |-- DrawAction.java
|   |   |                   |-- ImageMaker.java
|   |   |                   |-- PalTreeUtils.java
|   |   |                   |-- StreamGobbler.java
|   |   |                   |-- TreeParseException.java
|   |   |                   |-- UTree.java
|   |   |                   `-- Util.java
|   |   |-- resources
|   |   |   |-- MessageResources.properties
|   |   |   |-- MessageResources_en.properties
|   |   |   |-- RegisterUser-validation.xml
|   |   |   |-- log4j.xml
|   |   |   |-- org
|   |   |   |   `-- ngbw
|   |   |   |       `-- web
|   |   |   |           `-- actions
|   |   |   |               |-- RegisterUser-validation.xml
|   |   |   |               `-- package.properties
|   |   |   |-- struts-tools.xml
|   |   |   |-- struts.xml
|   |   |   `-- tools.properties
|   |   |-- ss_server
|   |   |   |-- Readme.txt
|   |   |   |-- log4j-1.2.12.jar
|   |   |   |-- ss_control
|   |   |   |-- ss_log4j.xml
|   |   |   `-- tl2.sh
|   |   `-- webapp
|   |       |-- META-INF
|   |       |   `-- MANIFEST.MF
|   |       |-- WEB-INF
|   |       |   |-- decorators.xml
|   |       |   |-- sitemesh.xml
|   |       |   |-- tiles.xml
|   |       |   |-- tld
|   |       |   |   |-- c.tld
|   |       |   |   `-- tiles-jsp.tld
|   |       |   `-- web.xml
|   |       |-- css
|   |       |   |-- blueprint
|   |       |   |   |-- ie.css
|   |       |   |   |-- plugins
|   |       |   |   |   `-- fancy-type
|   |       |   |   |       |-- readme.txt
|   |       |   |   |       `-- screen.css
|   |       |   |   |-- print.css
|   |       |   |   |-- screen.css
|   |       |   |   `-- src
|   |       |   |       |-- forms.css
|   |       |   |       |-- grid.css
|   |       |   |       |-- grid.png
|   |       |   |       |-- ie.css
|   |       |   |       |-- print.css
|   |       |   |       |-- reset.css
|   |       |   |       `-- typography.css
|   |       |   |-- cipres.css
|   |       |   |-- custom.css
|   |       |   |-- displaytag.css
|   |       |   `-- messages.css
|   |       |-- decorators
|   |       |   |-- default.jsp
|   |       |   `-- simple.jsp
|   |       |-- help
|   |       |   `-- cite.html
|   |       |-- images
|   |       |   |-- Calendar-July21-FINAL.jpg
|   |       |   |-- Poweredbyteragridsmall.jpg
|   |       |   |-- background.gif
|   |       |   |-- banner_nigms.gif
|   |       |   |-- bg_button_a.gif
|   |       |   |-- bg_button_div.gif
|   |       |   |-- button_closed.gif
|   |       |   |-- button_open.gif
|   |       |   |-- chromebg.gif
|   |       |   |-- closed.gif
|   |       |   |-- closed_box.png
|   |       |   |-- closedy2.png
|   |       |   |-- container-bg.gif
|   |       |   |-- database_seq_med.gif
|   |       |   |-- dna_seq_big.gif
|   |       |   |-- dna_seq_med.gif
|   |       |   |-- dna_seq_sm.gif
|   |       |   |-- doubleArrow.gif
|   |       |   |-- doubleArrow_b.gif
|   |       |   |-- doubleArrow_b_dark.gif
|   |       |   |-- doubleArrow_dark.gif
|   |       |   |-- favicon.ico
|   |       |   |-- folder_med.gif
|   |       |   |-- folder_sel_med.gif
|   |       |   |-- folder_sel_sm.gif
|   |       |   |-- folder_sm.gif
|   |       |   |-- footer_b.gif
|   |       |   |-- footer_bg.gif
|   |       |   |-- front_button_a.gif
|   |       |   |-- front_button_div.gif
|   |       |   |-- g_bwservice_tool_med.gif
|   |       |   |-- g_bwservice_tool_sm.gif
|   |       |   |-- headerBullet.gif
|   |       |   |-- ibm.gif
|   |       |   |-- ico_file_csv.png
|   |       |   |-- ico_file_excel.png
|   |       |   |-- ico_file_pdf.png
|   |       |   |-- ico_file_xml.png
|   |       |   |-- iconCalendar.gif
|   |       |   |-- iconEmail.gif
|   |       |   |-- iconHelp.gif
|   |       |   |-- iconInformation.gif
|   |       |   |-- iconWarning.gif
|   |       |   |-- info.png
|   |       |   |-- li-bullet.gif
|   |       |   |-- list.gif
|   |       |   |-- logo.gif
|   |       |   |-- ms_research.gif
|   |       |   |-- navInner_bg.gif
|   |       |   |-- nav_bg.gif
|   |       |   |-- new.gif
|   |       |   |-- newstructure.jpg
|   |       |   |-- off_bg.gif
|   |       |   |-- open.gif
|   |       |   |-- open_box.png
|   |       |   |-- opencq8.png
|   |       |   |-- page-head-bg.gif
|   |       |   |-- page.gif
|   |       |   |-- panel_bg.gif
|   |       |   |-- panel_bg_up.gif
|   |       |   |-- pw-icon.jpg
|   |       |   |-- report_issue_plain.gif
|   |       |   |-- request_feature_plain.gif
|   |       |   |-- results_doc_med.gif
|   |       |   |-- results_doc_sm.gif
|   |       |   |-- return.gif
|   |       |   |-- sample_boxshade_output.gif
|   |       |   |-- sample_form.gif
|   |       |   |-- sample_form_b.gif
|   |       |   |-- sdsc_logo.gif
|   |       |   |-- singleArrow.gif
|   |       |   |-- singleArrow_b.gif
|   |       |   |-- singleArrow_b_dark.gif
|   |       |   |-- singleArrow_dark.gif
|   |       |   |-- subscribe.gif
|   |       |   |-- tab-left-over.gif
|   |       |   |-- tab-left.gif
|   |       |   |-- tab-right-over.gif
|   |       |   |-- tab-right.gif
|   |       |   |-- tabs_left.gif
|   |       |   |-- tabs_left_over.gif
|   |       |   |-- tabs_right.gif
|   |       |   |-- tabs_right_over.gif
|   |       |   |-- tdRow.gif
|   |       |   |-- thRow.gif
|   |       |   |-- traffic-light-all.jpg
|   |       |   |-- ucsd_logo.gif
|   |       |   `-- wrap-bg.gif
|   |       |-- index.html
|   |       |-- index.jsp
|   |       |-- js
|   |       |   |-- animatedcollapse.js
|   |       |   |-- checkboxgroup.js
|   |       |   |-- global.js
|   |       |   |-- need-info.js
|   |       |   |-- ngbw.js
|   |       |   |-- simpletreemenu.js
|   |       |   |-- swami.js
|   |       |   `-- switchcontent.js
|   |       `-- pages
|   |           |-- common
|   |           |   |-- banner.jsp
|   |           |   |-- dataUploadLists.jsp
|   |           |   |-- datasetLists.jsp
|   |           |   |-- footer.jsp
|   |           |   |-- header.jsp
|   |           |   |-- loginBox.jsp
|   |           |   |-- menu.jsp
|   |           |   |-- messages-updated.jsp
|   |           |   |-- messages.jsp
|   |           |   |-- meta.jsp
|   |           |   |-- taglibs.jsp
|   |           |   `-- underconstruction.jsp
|   |           |-- default
|   |           |   |-- content.jsp
|   |           |   `-- navigation.jsp
|   |           |-- layouts
|   |           |   |-- forward.jsp
|   |           |   |-- mainLayout.jsp
|   |           |   |-- popupLayout.jsp
|   |           |   `-- popupLayoutEx.jsp
|   |           |-- static
|   |           |   |-- compatibility.jsp
|   |           |   |-- contact.jsp
|   |           |   |-- error.html
|   |           |   |-- faq.jsp
|   |           |   |-- funding.jsp
|   |           |   |-- help.jsp
|   |           |   |-- home.html
|   |           |   |-- links.jsp
|   |           |   |-- news.jsp
|   |           |   |-- publications.jsp
|   |           |   |-- tool
|   |           |   |   |-- blast2.html
|   |           |   |   |-- boxshade.html
|   |           |   |   |-- clique.html
|   |           |   |   |-- clustalw.html
|   |           |   |   |-- consense.html
|   |           |   |   |-- dnadist.html
|   |           |   |   |-- dnapars.html
|   |           |   |   |-- dollop.html
|   |           |   |   |-- mfold.html
|   |           |   |   |-- mix.html
|   |           |   |   |-- pars.html
|   |           |   |   |-- perl.pl
|   |           |   |   |-- protdist.html
|   |           |   |   |-- protpars.html
|   |           |   |   |-- psiblast.html
|   |           |   |   |-- seqboot.html
|   |           |   |   |-- tool_tests
|   |           |   |   |   |-- align_nuc_out1.txt
|   |           |   |   |   |-- alignn1_in.txt
|   |           |   |   |   |-- alignn2_in.txt
|   |           |   |   |   |-- blast2seqn1_in.txt
|   |           |   |   |   |-- blast2seqn2_in.txt
|   |           |   |   |   |-- blast2seqn_out1.txt
|   |           |   |   |   |-- blimps_in.txt
|   |           |   |   |   |-- blimps_out.txt
|   |           |   |   |   |-- clustal_profile_test_in1.aln
|   |           |   |   |   |-- clustal_profile_test_in2.aln
|   |           |   |   |   |-- clustal_profile_test_out1.aln
|   |           |   |   |   |-- clustal_seq_in.fasta
|   |           |   |   |   |-- clustal_test1.txt
|   |           |   |   |   |-- clustal_test1_out1.txt
|   |           |   |   |   |-- clustal_test_out2.txt
|   |           |   |   |   |-- clustalw_tree_in1.aln
|   |           |   |   |   |-- clustalw_tree_out1.ph
|   |           |   |   |   |-- clustalwdist_test_in_1.aln
|   |           |   |   |   |-- clustalwdist_test_out1.dst.txt
|   |           |   |   |   |-- clustalwdist_test_out1.ph.txt
|   |           |   |   |   |-- degapseqn_in.txt
|   |           |   |   |   |-- degapseqn_out.txt
|   |           |   |   |   |-- fastx_in.txt
|   |           |   |   |   |-- fastx_out.txt
|   |           |   |   |   |-- fasty_in.txt
|   |           |   |   |   |-- fasty_out.txt
|   |           |   |   |   |-- fingerprintscan_in.txt
|   |           |   |   |   |-- fingerprintscan_test_out1.txt
|   |           |   |   |   |-- hmmpfam_in.txt
|   |           |   |   |   |-- hmmpfam_out1.txt
|   |           |   |   |   |-- hth_input1.txt
|   |           |   |   |   |-- hth_output1.txt
|   |           |   |   |   |-- lalign1_in.txt
|   |           |   |   |   |-- lalign2_in.txt
|   |           |   |   |   |-- lalign_out1.txt
|   |           |   |   |   |-- mfoldtest1.pdf
|   |           |   |   |   |-- mfoldtest2.pdf
|   |           |   |   |   |-- mview.html
|   |           |   |   |   |-- mviewalign_in1.txt
|   |           |   |   |   |-- mviewalign_out1.html
|   |           |   |   |   |-- mviewblast_in1.txt
|   |           |   |   |   |-- mviewblast_out1.html
|   |           |   |   |   |-- pepinfo_in.txt
|   |           |   |   |   |-- pepstats_in.txt
|   |           |   |   |   |-- pepstats_out.txt
|   |           |   |   |   |-- pepwndow_in1.txt
|   |           |   |   |   |-- pfscan_in.txt
|   |           |   |   |   |-- pfscan_out.txt
|   |           |   |   |   |-- pfsearch_profile_in.txt
|   |           |   |   |   |-- phyml_input1.txt
|   |           |   |   |   |-- phyml_output_stats.txt
|   |           |   |   |   |-- phyml_output_trees.txt
|   |           |   |   |   |-- ppsearch_in.txt
|   |           |   |   |   |-- ppsearch_out.txt
|   |           |   |   |   |-- prosearch_in.txt
|   |           |   |   |   |-- prosearch_out.txt
|   |           |   |   |   |-- prss_out1.txt
|   |           |   |   |   |-- prssn1_in.txt
|   |           |   |   |   |-- prssn2_in.txt
|   |           |   |   |   |-- revseq_in.txt
|   |           |   |   |   |-- revseq_out.txt
|   |           |   |   |   |-- rpsblast_in.txt
|   |           |   |   |   |-- rpsblast_out.txt
|   |           |   |   |   |-- sixpack_in.txt
|   |           |   |   |   |-- sixpack_out.txt
|   |           |   |   |   |-- ssearch_in.txt
|   |           |   |   |   |-- ssearch_out.txt
|   |           |   |   |   |-- tacg_in.txt
|   |           |   |   |   |-- tacg_out.txt
|   |           |   |   |   |-- tfasta_in.txt
|   |           |   |   |   |-- tfasta_out1.txt
|   |           |   |   |   |-- tfastx_in.txt
|   |           |   |   |   |-- tfastx_out.txt
|   |           |   |   |   |-- tfasty_in.txt
|   |           |   |   |   |-- tfasty_out.txt
|   |           |   |   |   |-- tmap.1.png
|   |           |   |   |   `-- tmap1.txt
|   |           |   |   `-- unroot.html
|   |           |   `-- unavailable.html
|   |           |-- tool
|   |           |   |-- align.jsp
|   |           |   |-- beast_tg.jsp
|   |           |   |-- bl2seq.jsp
|   |           |   |-- blast2.jsp
|   |           |   |-- blastn.jsp
|   |           |   |-- blastp.jsp
|   |           |   |-- blastx.jsp
|   |           |   |-- blimps.jsp
|   |           |   |-- boxshade.jsp
|   |           |   |-- bucky.jsp
|   |           |   |-- clearcut.jsp
|   |           |   |-- clique.jsp
|   |           |   |-- clustalw.jsp
|   |           |   |-- clustalw_dist.jsp
|   |           |   |-- clustalw_n.jsp
|   |           |   |-- clustalw_p.jsp
|   |           |   |-- clustalw_profile.jsp
|   |           |   |-- clustalw_tree.jsp
|   |           |   |-- compass.jsp
|   |           |   |-- consense.jsp
|   |           |   |-- contralign.jsp
|   |           |   |-- degapseq.jsp
|   |           |   |-- dnadist.jsp
|   |           |   |-- dnapars.jsp
|   |           |   |-- dollop.jsp
|   |           |   |-- drawgram.jsp
|   |           |   |-- drawtree.jsp
|   |           |   |-- dssp.jsp
|   |           |   |-- epestfind.jsp
|   |           |   |-- eprimer3.jsp
|   |           |   |-- extractalign.jsp
|   |           |   |-- extractseq.jsp
|   |           |   |-- fasta_n.jsp
|   |           |   |-- fasta_p.jsp
|   |           |   |-- fastx.jsp
|   |           |   |-- fasty.jsp
|   |           |   |-- fingerprintscan.jsp
|   |           |   |-- fitch.jsp
|   |           |   |-- formatvalidator.jsp
|   |           |   |-- fsa.jsp
|   |           |   |-- garli.jsp
|   |           |   |-- garli2_tgb.jsp
|   |           |   |-- garli_abe.jsp
|   |           |   |-- garli_conf_creator.jsp
|   |           |   |-- garli_lonestar.jsp
|   |           |   |-- garli_tg.jsp
|   |           |   |-- helixturnhelix.jsp
|   |           |   |-- hmmpfam.jsp
|   |           |   |-- kitsch.jsp
|   |           |   |-- lalign.jsp
|   |           |   |-- mafft.jsp
|   |           |   |-- mafft_tg.jsp
|   |           |   |-- mafftnew.jsp
|   |           |   |-- mbsum.jsp
|   |           |   |-- merger.jsp
|   |           |   |-- mfold.jsp
|   |           |   |-- mix.jsp
|   |           |   |-- mrbayes.jsp
|   |           |   |-- mrbayes_abe.jsp
|   |           |   |-- mrbayes_lonestar.jsp
|   |           |   |-- mrbayeshybrid_abe.jsp
|   |           |   |-- mrbayeshybrid_tg.jsp
|   |           |   |-- msa.jsp
|   |           |   |-- muscle.jsp
|   |           |   |-- mview_alig.jsp
|   |           |   |-- mview_blast.jsp
|   |           |   |-- nclconverter.jsp
|   |           |   |-- neighbor.jsp
|   |           |   |-- new_tool.jsp
|   |           |   |-- pars.jsp
|   |           |   |-- paup.jsp
|   |           |   |-- pauprat.jsp
|   |           |   |-- pauprat_exp.jsp
|   |           |   |-- pepinfo.jsp
|   |           |   |-- pepstats.jsp
|   |           |   |-- pepwindow.jsp
|   |           |   |-- pfscan.jsp
|   |           |   |-- pfsearch.jsp
|   |           |   |-- phyml.jsp
|   |           |   |-- poy.jsp
|   |           |   |-- poy2.jsp
|   |           |   |-- ppsearch.jsp
|   |           |   |-- probalign.jsp
|   |           |   |-- probcons.jsp
|   |           |   |-- prosearch.jsp
|   |           |   |-- protdist.jsp
|   |           |   |-- proteus.jsp
|   |           |   |-- protpars.jsp
|   |           |   |-- prss.jsp
|   |           |   |-- psiblast.jsp
|   |           |   |-- psipred.jsp
|   |           |   |-- raxmlhpc.jsp
|   |           |   |-- raxmlhpc2.jsp
|   |           |   |-- raxmlhpc2_abe.jsp
|   |           |   |-- raxmlhpc2_abe727.jsp
|   |           |   |-- raxmlhpc2_abe_727.jsp
|   |           |   |-- raxmlhpc2_tg.jsp
|   |           |   |-- raxmlhpc2_tgb.jsp
|   |           |   |-- raxmlhpc2bb.jsp
|   |           |   |-- raxmlhpc_abe.jsp
|   |           |   |-- readseq.jsp
|   |           |   |-- restrict.jsp
|   |           |   |-- revseq.jsp
|   |           |   |-- rid3paup.jsp
|   |           |   |-- rid3raxml.jsp
|   |           |   |-- rpsblast.jsp
|   |           |   |-- saps.jsp
|   |           |   |-- seqboot.jsp
|   |           |   |-- seqretsplit.jsp
|   |           |   |-- sixpack.jsp
|   |           |   |-- sleep.jsp
|   |           |   |-- spidey.jsp
|   |           |   |-- ssearch_n.jsp
|   |           |   |-- ssearch_p.jsp
|   |           |   |-- tacg.jsp
|   |           |   |-- tblastn.jsp
|   |           |   |-- tblastx.jsp
|   |           |   |-- tfasta.jsp
|   |           |   |-- tfastx.jsp
|   |           |   |-- tfasty.jsp
|   |           |   |-- tmap.jsp
|   |           |   `-- unroot.jsp
|   |           `-- user
|   |               |-- data
|   |               |   |-- basicSearch.jsp
|   |               |   |-- dataList.jsp
|   |               |   |-- displayData.jsp
|   |               |   |-- displaySearchResult.jsp
|   |               |   |-- pasteForm.jsp
|   |               |   |-- resultsPage.jsp
|   |               |   |-- searchForm.jsp
|   |               |   |-- treedraw.jsp
|   |               |   `-- uploadForm.jsp
|   |               |-- displayTool.jsp
|   |               |-- folder
|   |               |   |-- displayFolder.jsp
|   |               |   |-- folderForm.jsp
|   |               |   |-- folderList.jsp
|   |               |   `-- importBwbData.jsp
|   |               |-- forgotPassword.jsp
|   |               |-- home.jsp
|   |               |-- login.jsp
|   |               |-- profile.jsp
|   |               |-- register.jsp
|   |               |-- statistics.jsp
|   |               |-- task
|   |               |   |-- displayInput.jsp
|   |               |   |-- displayOutput.jsp
|   |               |   |-- displayOutputList.jsp
|   |               |   |-- displayParameters.jsp
|   |               |   |-- displayTask.jsp
|   |               |   |-- displayTransformedOutput.jsp
|   |               |   |-- displayTransformedRecord.jsp
|   |               |   |-- displayWorkingDirectory.jsp
|   |               |   |-- outputForm.jsp
|   |               |   |-- selectData.jsp
|   |               |   |-- selectTool.jsp
|   |               |   |-- taskForm.jsp
|   |               |   |-- taskList.jsp
|   |               |   `-- taskSummary.jsp
|   |               |-- taskupdateerror.txt
|   |               |-- taskupdateok.txt
|   |               |-- tools.jsp
|   |               |-- updatePassword.jsp
|   |               `-- updateProfile.jsp
|   `-- test
|       `-- java
|           `-- org
|               `-- ngbw
|                   `-- web
|                       `-- controllers
|                           |-- TestController.java
|                           |-- TestDataFormatController.java
|                           |-- TestDatasetController.java
|                           |-- TestFolderController.java
|                           `-- TestSessionController.java
|-- target
|   |-- classes
|   |   |-- MessageResources.properties
|   |   |-- MessageResources_en.properties
|   |   |-- RegisterUser-validation.xml
|   |   |-- log4j.xml
|   |   |-- org
|   |   |   `-- ngbw
|   |   |       `-- web
|   |   |           |-- actions
|   |   |           |   |-- ArchiveManager$1.class
|   |   |           |   |-- ArchiveManager.class
|   |   |           |   |-- CreateData.class
|   |   |           |   |-- CreateTask.class
|   |   |           |   |-- DataManager.class
|   |   |           |   |-- DownloadAction.class
|   |   |           |   |-- FolderManager.class
|   |   |           |   |-- ManageTasks.class
|   |   |           |   |-- NgbwSupport.class
|   |   |           |   |-- ProfileManager.class
|   |   |           |   |-- RegisterStatistics.class
|   |   |           |   |-- RegisterUser-validation.xml
|   |   |           |   |-- RegisterUser.class
|   |   |           |   |-- SearchData.class
|   |   |           |   |-- SessionManager.class
|   |   |           |   |-- SetTaskOutput.class
|   |   |           |   |-- TaskUpdate.class
|   |   |           |   |-- ToolParameters.class
|   |   |           |   |-- ajax
|   |   |           |   |   |-- DataUploadLists.class
|   |   |           |   |   |-- DatasetLists.class
|   |   |           |   |   `-- ToggleFolder.class
|   |   |           |   |-- package.properties
|   |   |           |   `-- tool
|   |   |           |       |-- align.class
|   |   |           |       |-- beast_tg.class
|   |   |           |       |-- bl2seq.class
|   |   |           |       |-- blast2.class
|   |   |           |       |-- blastn.class
|   |   |           |       |-- blastp.class
|   |   |           |       |-- blastx.class
|   |   |           |       |-- blimps.class
|   |   |           |       |-- boxshade.class
|   |   |           |       |-- bucky.class
|   |   |           |       |-- clearcut.class
|   |   |           |       |-- clique.class
|   |   |           |       |-- clustalw.class
|   |   |           |       |-- clustalw_dist.class
|   |   |           |       |-- clustalw_n.class
|   |   |           |       |-- clustalw_p.class
|   |   |           |       |-- clustalw_profile.class
|   |   |           |       |-- clustalw_tree.class
|   |   |           |       |-- compass.class
|   |   |           |       |-- consense.class
|   |   |           |       |-- contralign.class
|   |   |           |       |-- degapseq.class
|   |   |           |       |-- dnadist.class
|   |   |           |       |-- dnapars.class
|   |   |           |       |-- dollop.class
|   |   |           |       |-- drawgram.class
|   |   |           |       |-- drawtree.class
|   |   |           |       |-- dssp.class
|   |   |           |       |-- epestfind.class
|   |   |           |       |-- eprimer3.class
|   |   |           |       |-- extractalign.class
|   |   |           |       |-- extractseq.class
|   |   |           |       |-- fasta_n.class
|   |   |           |       |-- fasta_p.class
|   |   |           |       |-- fastx.class
|   |   |           |       |-- fasty.class
|   |   |           |       |-- fingerprintscan.class
|   |   |           |       |-- fitch.class
|   |   |           |       |-- formatvalidator.class
|   |   |           |       |-- fsa.class
|   |   |           |       |-- garli.class
|   |   |           |       |-- garli2_tgb.class
|   |   |           |       |-- garli_abe.class
|   |   |           |       |-- garli_conf_creator.class
|   |   |           |       |-- garli_lonestar.class
|   |   |           |       |-- garli_tg.class
|   |   |           |       |-- helixturnhelix.class
|   |   |           |       |-- hmmpfam.class
|   |   |           |       |-- kitsch.class
|   |   |           |       |-- lalign.class
|   |   |           |       |-- mafft.class
|   |   |           |       |-- mafft_tg.class
|   |   |           |       |-- mafftnew.class
|   |   |           |       |-- mbsum.class
|   |   |           |       |-- merger.class
|   |   |           |       |-- mfold.class
|   |   |           |       |-- mix.class
|   |   |           |       |-- mrbayes.class
|   |   |           |       |-- mrbayes_abe.class
|   |   |           |       |-- mrbayes_lonestar.class
|   |   |           |       |-- mrbayeshybrid_abe.class
|   |   |           |       |-- mrbayeshybrid_tg.class
|   |   |           |       |-- msa.class
|   |   |           |       |-- muscle.class
|   |   |           |       |-- mview_alig.class
|   |   |           |       |-- mview_blast.class
|   |   |           |       |-- nclconverter.class
|   |   |           |       |-- neighbor.class
|   |   |           |       |-- new_tool.class
|   |   |           |       |-- pars.class
|   |   |           |       |-- paup.class
|   |   |           |       |-- pauprat.class
|   |   |           |       |-- pauprat_exp.class
|   |   |           |       |-- pepinfo.class
|   |   |           |       |-- pepstats.class
|   |   |           |       |-- pepwindow.class
|   |   |           |       |-- pfscan.class
|   |   |           |       |-- pfsearch.class
|   |   |           |       |-- phyml.class
|   |   |           |       |-- poy.class
|   |   |           |       |-- poy2.class
|   |   |           |       |-- ppsearch.class
|   |   |           |       |-- probalign.class
|   |   |           |       |-- probcons.class
|   |   |           |       |-- prosearch.class
|   |   |           |       |-- protdist.class
|   |   |           |       |-- proteus.class
|   |   |           |       |-- protpars.class
|   |   |           |       |-- prss.class
|   |   |           |       |-- psiblast.class
|   |   |           |       |-- psipred.class
|   |   |           |       |-- raxmlhpc.class
|   |   |           |       |-- raxmlhpc2.class
|   |   |           |       |-- raxmlhpc2_abe.class
|   |   |           |       |-- raxmlhpc2_abe727.class
|   |   |           |       |-- raxmlhpc2_abe_727.class
|   |   |           |       |-- raxmlhpc2_tg.class
|   |   |           |       |-- raxmlhpc2_tgb.class
|   |   |           |       |-- raxmlhpc2bb.class
|   |   |           |       |-- raxmlhpc_abe.class
|   |   |           |       |-- readseq.class
|   |   |           |       |-- restrict.class
|   |   |           |       |-- revseq.class
|   |   |           |       |-- rid3paup.class
|   |   |           |       |-- rid3raxml.class
|   |   |           |       |-- rpsblast.class
|   |   |           |       |-- saps.class
|   |   |           |       |-- seqboot.class
|   |   |           |       |-- seqretsplit.class
|   |   |           |       |-- sixpack.class
|   |   |           |       |-- sleep.class
|   |   |           |       |-- spidey.class
|   |   |           |       |-- ssearch_n.class
|   |   |           |       |-- ssearch_p.class
|   |   |           |       |-- tacg.class
|   |   |           |       |-- tblastn.class
|   |   |           |       |-- tblastx.class
|   |   |           |       |-- tfasta.class
|   |   |           |       |-- tfastx.class
|   |   |           |       |-- tfasty.class
|   |   |           |       |-- tmap.class
|   |   |           |       `-- unroot.class
|   |   |           |-- controllers
|   |   |           |   |-- DataController.class
|   |   |           |   |-- DataFormatController.class
|   |   |           |   |-- DatasetController.class
|   |   |           |   |-- FolderController.class
|   |   |           |   |-- RecordTypeController.class
|   |   |           |   `-- SessionController.class
|   |   |           |-- interceptors
|   |   |           |   |-- AuthenticationInterceptor.class
|   |   |           |   |-- NavigationInterceptor.class
|   |   |           |   `-- SessionListener.class
|   |   |           |-- model
|   |   |           |   |-- Page.class
|   |   |           |   |-- Tab.class
|   |   |           |   |-- TabbedPanel.class
|   |   |           |   `-- impl
|   |   |           |       |-- ConceptComparator.class
|   |   |           |       |-- DataRecordPage.class
|   |   |           |       |-- ListPage.class
|   |   |           |       |-- RecordFieldTypeComparator.class
|   |   |           |       |-- ToolComparator.class
|   |   |           |       `-- tool
|   |   |           |           |-- alignValidator.class
|   |   |           |           |-- beast_tgValidator.class
|   |   |           |           |-- bl2seqValidator.class
|   |   |           |           |-- blast2Validator.class
|   |   |           |           |-- blastnValidator.class
|   |   |           |           |-- blastpValidator.class
|   |   |           |           |-- blastxValidator.class
|   |   |           |           |-- blimpsValidator.class
|   |   |           |           |-- boxshadeValidator.class
|   |   |           |           |-- buckyValidator.class
|   |   |           |           |-- clearcutValidator.class
|   |   |           |           |-- cliqueValidator.class
|   |   |           |           |-- clustalwValidator.class
|   |   |           |           |-- clustalw_distValidator.class
|   |   |           |           |-- clustalw_nValidator.class
|   |   |           |           |-- clustalw_pValidator.class
|   |   |           |           |-- clustalw_profileValidator.class
|   |   |           |           |-- clustalw_treeValidator.class
|   |   |           |           |-- compassValidator.class
|   |   |           |           |-- consenseValidator.class
|   |   |           |           |-- contralignValidator.class
|   |   |           |           |-- degapseqValidator.class
|   |   |           |           |-- dnadistValidator.class
|   |   |           |           |-- dnaparsValidator.class
|   |   |           |           |-- dollopValidator.class
|   |   |           |           |-- drawgramValidator.class
|   |   |           |           |-- drawtreeValidator.class
|   |   |           |           |-- dsspValidator.class
|   |   |           |           |-- epestfindValidator.class
|   |   |           |           |-- eprimer3Validator.class
|   |   |           |           |-- extractalignValidator.class
|   |   |           |           |-- extractseqValidator.class
|   |   |           |           |-- fasta_nValidator.class
|   |   |           |           |-- fasta_pValidator.class
|   |   |           |           |-- fastxValidator.class
|   |   |           |           |-- fastyValidator.class
|   |   |           |           |-- fingerprintscanValidator.class
|   |   |           |           |-- fitchValidator.class
|   |   |           |           |-- formatvalidatorValidator.class
|   |   |           |           |-- fsaValidator.class
|   |   |           |           |-- garli2_tgbValidator.class
|   |   |           |           |-- garliValidator.class
|   |   |           |           |-- garli_abeValidator.class
|   |   |           |           |-- garli_conf_creatorValidator.class
|   |   |           |           |-- garli_lonestarValidator.class
|   |   |           |           |-- garli_tgValidator.class
|   |   |           |           |-- helixturnhelixValidator.class
|   |   |           |           |-- hmmpfamValidator.class
|   |   |           |           |-- kitschValidator.class
|   |   |           |           |-- lalignValidator.class
|   |   |           |           |-- mafftValidator.class
|   |   |           |           |-- mafft_tgValidator.class
|   |   |           |           |-- mafftnewValidator.class
|   |   |           |           |-- mbsumValidator.class
|   |   |           |           |-- mergerValidator.class
|   |   |           |           |-- mfoldValidator.class
|   |   |           |           |-- mixValidator.class
|   |   |           |           |-- mrbayesValidator.class
|   |   |           |           |-- mrbayes_abeValidator.class
|   |   |           |           |-- mrbayes_lonestarValidator.class
|   |   |           |           |-- mrbayeshybrid_abeValidator.class
|   |   |           |           |-- mrbayeshybrid_tgValidator.class
|   |   |           |           |-- msaValidator.class
|   |   |           |           |-- muscleValidator.class
|   |   |           |           |-- mview_aligValidator.class
|   |   |           |           |-- mview_blastValidator.class
|   |   |           |           |-- nclconverterValidator.class
|   |   |           |           |-- neighborValidator.class
|   |   |           |           |-- new_toolValidator.class
|   |   |           |           |-- parsValidator.class
|   |   |           |           |-- paupValidator.class
|   |   |           |           |-- paupratValidator.class
|   |   |           |           |-- pauprat_expValidator.class
|   |   |           |           |-- pepinfoValidator.class
|   |   |           |           |-- pepstatsValidator.class
|   |   |           |           |-- pepwindowValidator.class
|   |   |           |           |-- pfscanValidator.class
|   |   |           |           |-- pfsearchValidator.class
|   |   |           |           |-- phymlValidator.class
|   |   |           |           |-- poy2Validator.class
|   |   |           |           |-- poyValidator.class
|   |   |           |           |-- ppsearchValidator.class
|   |   |           |           |-- probalignValidator.class
|   |   |           |           |-- probconsValidator.class
|   |   |           |           |-- prosearchValidator.class
|   |   |           |           |-- protdistValidator.class
|   |   |           |           |-- proteusValidator.class
|   |   |           |           |-- protparsValidator.class
|   |   |           |           |-- prssValidator.class
|   |   |           |           |-- psiblastValidator.class
|   |   |           |           |-- psipredValidator.class
|   |   |           |           |-- raxmlhpc2Validator.class
|   |   |           |           |-- raxmlhpc2_abe727Validator.class
|   |   |           |           |-- raxmlhpc2_abeValidator.class
|   |   |           |           |-- raxmlhpc2_abe_727Validator.class
|   |   |           |           |-- raxmlhpc2_tgValidator.class
|   |   |           |           |-- raxmlhpc2_tgbValidator.class
|   |   |           |           |-- raxmlhpc2bbValidator.class
|   |   |           |           |-- raxmlhpcValidator.class
|   |   |           |           |-- raxmlhpc_abeValidator.class
|   |   |           |           |-- readseqValidator.class
|   |   |           |           |-- restrictValidator.class
|   |   |           |           |-- revseqValidator.class
|   |   |           |           |-- rid3paupValidator.class
|   |   |           |           |-- rid3raxmlValidator.class
|   |   |           |           |-- rpsblastValidator.class
|   |   |           |           |-- sapsValidator.class
|   |   |           |           |-- seqbootValidator.class
|   |   |           |           |-- seqretsplitValidator.class
|   |   |           |           |-- sixpackValidator.class
|   |   |           |           |-- sleepValidator.class
|   |   |           |           |-- spideyValidator.class
|   |   |           |           |-- ssearch_nValidator.class
|   |   |           |           |-- ssearch_pValidator.class
|   |   |           |           |-- tacgValidator.class
|   |   |           |           |-- tblastnValidator.class
|   |   |           |           |-- tblastxValidator.class
|   |   |           |           |-- tfastaValidator.class
|   |   |           |           |-- tfastxValidator.class
|   |   |           |           |-- tfastyValidator.class
|   |   |           |           |-- tmapValidator.class
|   |   |           |           `-- unrootValidator.class
|   |   |           `-- treeimage
|   |   |               |-- DownloadAction.class
|   |   |               |-- DrawAction.class
|   |   |               |-- ImageMaker$NodeInfo.class
|   |   |               |-- ImageMaker.class
|   |   |               |-- PalTreeUtils.class
|   |   |               |-- StreamGobbler.class
|   |   |               |-- TreeParseException.class
|   |   |               |-- UTree.class
|   |   |               `-- Util.class
|   |   |-- struts-tools.xml
|   |   |-- struts.xml
|   |   `-- tools.properties
|   |-- portal2
|   |   |-- META-INF
|   |   |   `-- MANIFEST.MF
|   |   |-- WEB-INF
|   |   |   |-- classes
|   |   |   |   |-- MessageResources.properties
|   |   |   |   |-- MessageResources_en.properties
|   |   |   |   |-- RegisterUser-validation.xml
|   |   |   |   |-- log4j.xml
|   |   |   |   |-- org
|   |   |   |   |   `-- ngbw
|   |   |   |   |       `-- web
|   |   |   |   |           |-- actions
|   |   |   |   |           |   |-- ArchiveManager$1.class
|   |   |   |   |           |   |-- ArchiveManager.class
|   |   |   |   |           |   |-- CreateData.class
|   |   |   |   |           |   |-- CreateTask.class
|   |   |   |   |           |   |-- DataManager.class
|   |   |   |   |           |   |-- DownloadAction.class
|   |   |   |   |           |   |-- FolderManager.class
|   |   |   |   |           |   |-- ManageTasks.class
|   |   |   |   |           |   |-- NgbwSupport.class
|   |   |   |   |           |   |-- ProfileManager.class
|   |   |   |   |           |   |-- RegisterStatistics.class
|   |   |   |   |           |   |-- RegisterUser-validation.xml
|   |   |   |   |           |   |-- RegisterUser.class
|   |   |   |   |           |   |-- SearchData.class
|   |   |   |   |           |   |-- SessionManager.class
|   |   |   |   |           |   |-- SetTaskOutput.class
|   |   |   |   |           |   |-- TaskUpdate.class
|   |   |   |   |           |   |-- ToolParameters.class
|   |   |   |   |           |   |-- ajax
|   |   |   |   |           |   |   |-- DataUploadLists.class
|   |   |   |   |           |   |   |-- DatasetLists.class
|   |   |   |   |           |   |   `-- ToggleFolder.class
|   |   |   |   |           |   |-- package.properties
|   |   |   |   |           |   `-- tool
|   |   |   |   |           |       |-- align.class
|   |   |   |   |           |       |-- beast_tg.class
|   |   |   |   |           |       |-- bl2seq.class
|   |   |   |   |           |       |-- blast2.class
|   |   |   |   |           |       |-- blastn.class
|   |   |   |   |           |       |-- blastp.class
|   |   |   |   |           |       |-- blastx.class
|   |   |   |   |           |       |-- blimps.class
|   |   |   |   |           |       |-- boxshade.class
|   |   |   |   |           |       |-- bucky.class
|   |   |   |   |           |       |-- clearcut.class
|   |   |   |   |           |       |-- clique.class
|   |   |   |   |           |       |-- clustalw.class
|   |   |   |   |           |       |-- clustalw_dist.class
|   |   |   |   |           |       |-- clustalw_n.class
|   |   |   |   |           |       |-- clustalw_p.class
|   |   |   |   |           |       |-- clustalw_profile.class
|   |   |   |   |           |       |-- clustalw_tree.class
|   |   |   |   |           |       |-- compass.class
|   |   |   |   |           |       |-- consense.class
|   |   |   |   |           |       |-- contralign.class
|   |   |   |   |           |       |-- degapseq.class
|   |   |   |   |           |       |-- dnadist.class
|   |   |   |   |           |       |-- dnapars.class
|   |   |   |   |           |       |-- dollop.class
|   |   |   |   |           |       |-- drawgram.class
|   |   |   |   |           |       |-- drawtree.class
|   |   |   |   |           |       |-- dssp.class
|   |   |   |   |           |       |-- epestfind.class
|   |   |   |   |           |       |-- eprimer3.class
|   |   |   |   |           |       |-- extractalign.class
|   |   |   |   |           |       |-- extractseq.class
|   |   |   |   |           |       |-- fasta_n.class
|   |   |   |   |           |       |-- fasta_p.class
|   |   |   |   |           |       |-- fastx.class
|   |   |   |   |           |       |-- fasty.class
|   |   |   |   |           |       |-- fingerprintscan.class
|   |   |   |   |           |       |-- fitch.class
|   |   |   |   |           |       |-- formatvalidator.class
|   |   |   |   |           |       |-- fsa.class
|   |   |   |   |           |       |-- garli.class
|   |   |   |   |           |       |-- garli2_tgb.class
|   |   |   |   |           |       |-- garli_abe.class
|   |   |   |   |           |       |-- garli_conf_creator.class
|   |   |   |   |           |       |-- garli_lonestar.class
|   |   |   |   |           |       |-- garli_tg.class
|   |   |   |   |           |       |-- helixturnhelix.class
|   |   |   |   |           |       |-- hmmpfam.class
|   |   |   |   |           |       |-- kitsch.class
|   |   |   |   |           |       |-- lalign.class
|   |   |   |   |           |       |-- mafft.class
|   |   |   |   |           |       |-- mafft_tg.class
|   |   |   |   |           |       |-- mafftnew.class
|   |   |   |   |           |       |-- mbsum.class
|   |   |   |   |           |       |-- merger.class
|   |   |   |   |           |       |-- mfold.class
|   |   |   |   |           |       |-- mix.class
|   |   |   |   |           |       |-- mrbayes.class
|   |   |   |   |           |       |-- mrbayes_abe.class
|   |   |   |   |           |       |-- mrbayes_lonestar.class
|   |   |   |   |           |       |-- mrbayeshybrid_abe.class
|   |   |   |   |           |       |-- mrbayeshybrid_tg.class
|   |   |   |   |           |       |-- msa.class
|   |   |   |   |           |       |-- muscle.class
|   |   |   |   |           |       |-- mview_alig.class
|   |   |   |   |           |       |-- mview_blast.class
|   |   |   |   |           |       |-- nclconverter.class
|   |   |   |   |           |       |-- neighbor.class
|   |   |   |   |           |       |-- new_tool.class
|   |   |   |   |           |       |-- pars.class
|   |   |   |   |           |       |-- paup.class
|   |   |   |   |           |       |-- pauprat.class
|   |   |   |   |           |       |-- pauprat_exp.class
|   |   |   |   |           |       |-- pepinfo.class
|   |   |   |   |           |       |-- pepstats.class
|   |   |   |   |           |       |-- pepwindow.class
|   |   |   |   |           |       |-- pfscan.class
|   |   |   |   |           |       |-- pfsearch.class
|   |   |   |   |           |       |-- phyml.class
|   |   |   |   |           |       |-- poy.class
|   |   |   |   |           |       |-- poy2.class
|   |   |   |   |           |       |-- ppsearch.class
|   |   |   |   |           |       |-- probalign.class
|   |   |   |   |           |       |-- probcons.class
|   |   |   |   |           |       |-- prosearch.class
|   |   |   |   |           |       |-- protdist.class
|   |   |   |   |           |       |-- proteus.class
|   |   |   |   |           |       |-- protpars.class
|   |   |   |   |           |       |-- prss.class
|   |   |   |   |           |       |-- psiblast.class
|   |   |   |   |           |       |-- psipred.class
|   |   |   |   |           |       |-- raxmlhpc.class
|   |   |   |   |           |       |-- raxmlhpc2.class
|   |   |   |   |           |       |-- raxmlhpc2_abe.class
|   |   |   |   |           |       |-- raxmlhpc2_abe727.class
|   |   |   |   |           |       |-- raxmlhpc2_abe_727.class
|   |   |   |   |           |       |-- raxmlhpc2_tg.class
|   |   |   |   |           |       |-- raxmlhpc2_tgb.class
|   |   |   |   |           |       |-- raxmlhpc2bb.class
|   |   |   |   |           |       |-- raxmlhpc_abe.class
|   |   |   |   |           |       |-- readseq.class
|   |   |   |   |           |       |-- restrict.class
|   |   |   |   |           |       |-- revseq.class
|   |   |   |   |           |       |-- rid3paup.class
|   |   |   |   |           |       |-- rid3raxml.class
|   |   |   |   |           |       |-- rpsblast.class
|   |   |   |   |           |       |-- saps.class
|   |   |   |   |           |       |-- seqboot.class
|   |   |   |   |           |       |-- seqretsplit.class
|   |   |   |   |           |       |-- sixpack.class
|   |   |   |   |           |       |-- sleep.class
|   |   |   |   |           |       |-- spidey.class
|   |   |   |   |           |       |-- ssearch_n.class
|   |   |   |   |           |       |-- ssearch_p.class
|   |   |   |   |           |       |-- tacg.class
|   |   |   |   |           |       |-- tblastn.class
|   |   |   |   |           |       |-- tblastx.class
|   |   |   |   |           |       |-- tfasta.class
|   |   |   |   |           |       |-- tfastx.class
|   |   |   |   |           |       |-- tfasty.class
|   |   |   |   |           |       |-- tmap.class
|   |   |   |   |           |       `-- unroot.class
|   |   |   |   |           |-- controllers
|   |   |   |   |           |   |-- DataController.class
|   |   |   |   |           |   |-- DataFormatController.class
|   |   |   |   |           |   |-- DatasetController.class
|   |   |   |   |           |   |-- FolderController.class
|   |   |   |   |           |   |-- RecordTypeController.class
|   |   |   |   |           |   `-- SessionController.class
|   |   |   |   |           |-- interceptors
|   |   |   |   |           |   |-- AuthenticationInterceptor.class
|   |   |   |   |           |   |-- NavigationInterceptor.class
|   |   |   |   |           |   `-- SessionListener.class
|   |   |   |   |           |-- model
|   |   |   |   |           |   |-- Page.class
|   |   |   |   |           |   |-- Tab.class
|   |   |   |   |           |   |-- TabbedPanel.class
|   |   |   |   |           |   `-- impl
|   |   |   |   |           |       |-- ConceptComparator.class
|   |   |   |   |           |       |-- DataRecordPage.class
|   |   |   |   |           |       |-- ListPage.class
|   |   |   |   |           |       |-- RecordFieldTypeComparator.class
|   |   |   |   |           |       |-- ToolComparator.class
|   |   |   |   |           |       `-- tool
|   |   |   |   |           |           |-- alignValidator.class
|   |   |   |   |           |           |-- beast_tgValidator.class
|   |   |   |   |           |           |-- bl2seqValidator.class
|   |   |   |   |           |           |-- blast2Validator.class
|   |   |   |   |           |           |-- blastnValidator.class
|   |   |   |   |           |           |-- blastpValidator.class
|   |   |   |   |           |           |-- blastxValidator.class
|   |   |   |   |           |           |-- blimpsValidator.class
|   |   |   |   |           |           |-- boxshadeValidator.class
|   |   |   |   |           |           |-- buckyValidator.class
|   |   |   |   |           |           |-- clearcutValidator.class
|   |   |   |   |           |           |-- cliqueValidator.class
|   |   |   |   |           |           |-- clustalwValidator.class
|   |   |   |   |           |           |-- clustalw_distValidator.class
|   |   |   |   |           |           |-- clustalw_nValidator.class
|   |   |   |   |           |           |-- clustalw_pValidator.class
|   |   |   |   |           |           |-- clustalw_profileValidator.class
|   |   |   |   |           |           |-- clustalw_treeValidator.class
|   |   |   |   |           |           |-- compassValidator.class
|   |   |   |   |           |           |-- consenseValidator.class
|   |   |   |   |           |           |-- contralignValidator.class
|   |   |   |   |           |           |-- degapseqValidator.class
|   |   |   |   |           |           |-- dnadistValidator.class
|   |   |   |   |           |           |-- dnaparsValidator.class
|   |   |   |   |           |           |-- dollopValidator.class
|   |   |   |   |           |           |-- drawgramValidator.class
|   |   |   |   |           |           |-- drawtreeValidator.class
|   |   |   |   |           |           |-- dsspValidator.class
|   |   |   |   |           |           |-- epestfindValidator.class
|   |   |   |   |           |           |-- eprimer3Validator.class
|   |   |   |   |           |           |-- extractalignValidator.class
|   |   |   |   |           |           |-- extractseqValidator.class
|   |   |   |   |           |           |-- fasta_nValidator.class
|   |   |   |   |           |           |-- fasta_pValidator.class
|   |   |   |   |           |           |-- fastxValidator.class
|   |   |   |   |           |           |-- fastyValidator.class
|   |   |   |   |           |           |-- fingerprintscanValidator.class
|   |   |   |   |           |           |-- fitchValidator.class
|   |   |   |   |           |           |-- formatvalidatorValidator.class
|   |   |   |   |           |           |-- fsaValidator.class
|   |   |   |   |           |           |-- garli2_tgbValidator.class
|   |   |   |   |           |           |-- garliValidator.class
|   |   |   |   |           |           |-- garli_abeValidator.class
|   |   |   |   |           |           |-- garli_conf_creatorValidator.class
|   |   |   |   |           |           |-- garli_lonestarValidator.class
|   |   |   |   |           |           |-- garli_tgValidator.class
|   |   |   |   |           |           |-- helixturnhelixValidator.class
|   |   |   |   |           |           |-- hmmpfamValidator.class
|   |   |   |   |           |           |-- kitschValidator.class
|   |   |   |   |           |           |-- lalignValidator.class
|   |   |   |   |           |           |-- mafftValidator.class
|   |   |   |   |           |           |-- mafft_tgValidator.class
|   |   |   |   |           |           |-- mafftnewValidator.class
|   |   |   |   |           |           |-- mbsumValidator.class
|   |   |   |   |           |           |-- mergerValidator.class
|   |   |   |   |           |           |-- mfoldValidator.class
|   |   |   |   |           |           |-- mixValidator.class
|   |   |   |   |           |           |-- mrbayesValidator.class
|   |   |   |   |           |           |-- mrbayes_abeValidator.class
|   |   |   |   |           |           |-- mrbayes_lonestarValidator.class
|   |   |   |   |           |           |-- mrbayeshybrid_abeValidator.class
|   |   |   |   |           |           |-- mrbayeshybrid_tgValidator.class
|   |   |   |   |           |           |-- msaValidator.class
|   |   |   |   |           |           |-- muscleValidator.class
|   |   |   |   |           |           |-- mview_aligValidator.class
|   |   |   |   |           |           |-- mview_blastValidator.class
|   |   |   |   |           |           |-- nclconverterValidator.class
|   |   |   |   |           |           |-- neighborValidator.class
|   |   |   |   |           |           |-- new_toolValidator.class
|   |   |   |   |           |           |-- parsValidator.class
|   |   |   |   |           |           |-- paupValidator.class
|   |   |   |   |           |           |-- paupratValidator.class
|   |   |   |   |           |           |-- pauprat_expValidator.class
|   |   |   |   |           |           |-- pepinfoValidator.class
|   |   |   |   |           |           |-- pepstatsValidator.class
|   |   |   |   |           |           |-- pepwindowValidator.class
|   |   |   |   |           |           |-- pfscanValidator.class
|   |   |   |   |           |           |-- pfsearchValidator.class
|   |   |   |   |           |           |-- phymlValidator.class
|   |   |   |   |           |           |-- poy2Validator.class
|   |   |   |   |           |           |-- poyValidator.class
|   |   |   |   |           |           |-- ppsearchValidator.class
|   |   |   |   |           |           |-- probalignValidator.class
|   |   |   |   |           |           |-- probconsValidator.class
|   |   |   |   |           |           |-- prosearchValidator.class
|   |   |   |   |           |           |-- protdistValidator.class
|   |   |   |   |           |           |-- proteusValidator.class
|   |   |   |   |           |           |-- protparsValidator.class
|   |   |   |   |           |           |-- prssValidator.class
|   |   |   |   |           |           |-- psiblastValidator.class
|   |   |   |   |           |           |-- psipredValidator.class
|   |   |   |   |           |           |-- raxmlhpc2Validator.class
|   |   |   |   |           |           |-- raxmlhpc2_abe727Validator.class
|   |   |   |   |           |           |-- raxmlhpc2_abeValidator.class
|   |   |   |   |           |           |-- raxmlhpc2_abe_727Validator.class
|   |   |   |   |           |           |-- raxmlhpc2_tgValidator.class
|   |   |   |   |           |           |-- raxmlhpc2_tgbValidator.class
|   |   |   |   |           |           |-- raxmlhpc2bbValidator.class
|   |   |   |   |           |           |-- raxmlhpcValidator.class
|   |   |   |   |           |           |-- raxmlhpc_abeValidator.class
|   |   |   |   |           |           |-- readseqValidator.class
|   |   |   |   |           |           |-- restrictValidator.class
|   |   |   |   |           |           |-- revseqValidator.class
|   |   |   |   |           |           |-- rid3paupValidator.class
|   |   |   |   |           |           |-- rid3raxmlValidator.class
|   |   |   |   |           |           |-- rpsblastValidator.class
|   |   |   |   |           |           |-- sapsValidator.class
|   |   |   |   |           |           |-- seqbootValidator.class
|   |   |   |   |           |           |-- seqretsplitValidator.class
|   |   |   |   |           |           |-- sixpackValidator.class
|   |   |   |   |           |           |-- sleepValidator.class
|   |   |   |   |           |           |-- spideyValidator.class
|   |   |   |   |           |           |-- ssearch_nValidator.class
|   |   |   |   |           |           |-- ssearch_pValidator.class
|   |   |   |   |           |           |-- tacgValidator.class
|   |   |   |   |           |           |-- tblastnValidator.class
|   |   |   |   |           |           |-- tblastxValidator.class
|   |   |   |   |           |           |-- tfastaValidator.class
|   |   |   |   |           |           |-- tfastxValidator.class
|   |   |   |   |           |           |-- tfastyValidator.class
|   |   |   |   |           |           |-- tmapValidator.class
|   |   |   |   |           |           `-- unrootValidator.class
|   |   |   |   |           `-- treeimage
|   |   |   |   |               |-- DownloadAction.class
|   |   |   |   |               |-- DrawAction.class
|   |   |   |   |               |-- ImageMaker$NodeInfo.class
|   |   |   |   |               |-- ImageMaker.class
|   |   |   |   |               |-- PalTreeUtils.class
|   |   |   |   |               |-- StreamGobbler.class
|   |   |   |   |               |-- TreeParseException.class
|   |   |   |   |               |-- UTree.class
|   |   |   |   |               `-- Util.class
|   |   |   |   |-- struts-tools.xml
|   |   |   |   |-- struts.xml
|   |   |   |   `-- tools.properties
|   |   |   |-- decorators.xml
|   |   |   |-- lib
|   |   |   |   |-- activation-1.1.jar
|   |   |   |   |-- aopalliance-1.0.jar
|   |   |   |   |-- c3p0-0.9.1.2.jar
|   |   |   |   |-- cog-jglobus-gt4.jar
|   |   |   |   |-- commons-beanutils-1.7.0.jar
|   |   |   |   |-- commons-codec-1.3-gt4.jar
|   |   |   |   |-- commons-collections-3.1.jar
|   |   |   |   |-- commons-digester-1.7.jar
|   |   |   |   |-- commons-fileupload-1.1.1.jar
|   |   |   |   |-- commons-io-1.1.jar
|   |   |   |   |-- commons-lang-2.3.jar
|   |   |   |   |-- commons-logging-1.1.1.jar
|   |   |   |   |-- commons-logging-api-1.1.jar
|   |   |   |   |-- commons-net-1.4.1.jar
|   |   |   |   |-- cryptix-asn1-gt4.jar
|   |   |   |   |-- cryptix32-gt4.jar
|   |   |   |   |-- displaytag-1.2.jar
|   |   |   |   |-- drmaa-0.5.jar
|   |   |   |   |-- freemarker-2.3.16.jar
|   |   |   |   |-- globus-opensaml-1.1-gt4.jar
|   |   |   |   |-- gridshib-common-0_5_0-gt4.jar
|   |   |   |   |-- gridshib-saml-tools-0_5_0-gt4.jar
|   |   |   |   |-- itext-1.3.jar
|   |   |   |   |-- javassist-3.7.ga.jar
|   |   |   |   |-- jaxb-api-2.1.jar
|   |   |   |   |-- jaxb-impl-2.1.jar
|   |   |   |   |-- jaxb-xjc-2.1.2.jar
|   |   |   |   |-- jce-jdk13-125-gt4.jar
|   |   |   |   |-- jcl104-over-slf4j-1.4.2.jar
|   |   |   |   |-- jsp-api-2.0.jar
|   |   |   |   |-- jsr173-1.0.jar
|   |   |   |   |-- jstl-1.1.2.jar
|   |   |   |   |-- log4j-1.2.14.jar
|   |   |   |   |-- lucene-core-2.3.2.jar
|   |   |   |   |-- mail-1.4.jar
|   |   |   |   |-- mailservice-1.0.jar
|   |   |   |   |-- mysql-connector-java-5.1.5.jar
|   |   |   |   |-- ognl-3.0.jar
|   |   |   |   |-- oro-2.0.8.jar
|   |   |   |   |-- pal-1.5.1-modified-1.jar
|   |   |   |   |-- puretls-gt4.jar
|   |   |   |   |-- sdk-2.0.jar
|   |   |   |   |-- servlet-api-2.4.jar
|   |   |   |   |-- sitemesh-2.4.2.jar
|   |   |   |   |-- slf4j-api-1.4.2.jar
|   |   |   |   |-- slf4j-log4j12-1.4.2.jar
|   |   |   |   |-- spring-2.5.6.jar
|   |   |   |   |-- spring-beans-2.5.6.jar
|   |   |   |   |-- spring-context-2.5.6.jar
|   |   |   |   |-- spring-context-support-2.5.6.jar
|   |   |   |   |-- spring-core-2.5.6.jar
|   |   |   |   |-- spring-web-2.5.6.jar
|   |   |   |   |-- spring-webmvc-2.5.6.jar
|   |   |   |   |-- standard-1.1.2.jar
|   |   |   |   |-- stax-api-1.0-2.jar
|   |   |   |   |-- struts-menu-2.4.3.jar
|   |   |   |   |-- struts2-config-browser-plugin-2.2.1.jar
|   |   |   |   |-- struts2-core-2.2.1.jar
|   |   |   |   |-- struts2-jasperreports-plugin-2.2.1.jar
|   |   |   |   |-- struts2-jfreechart-plugin-2.2.1.jar
|   |   |   |   |-- struts2-pell-multipart-plugin-2.2.1.jar
|   |   |   |   |-- struts2-sitegraph-plugin-2.2.1.jar
|   |   |   |   |-- struts2-sitemesh-plugin-2.2.1.jar
|   |   |   |   |-- struts2-tiles-plugin-2.2.1.jar
|   |   |   |   |-- tiles-api-2.0.6.jar
|   |   |   |   |-- tiles-core-2.0.6.jar
|   |   |   |   |-- tiles-jsp-2.0.6.jar
|   |   |   |   |-- trilead-ssh2-213.jar
|   |   |   |   |-- velocity-1.4.jar
|   |   |   |   |-- velocity-dep-1.4.jar
|   |   |   |   |-- velocity-tools-view-1.0.jar
|   |   |   |   |-- xalan-gt4.jar
|   |   |   |   |-- xmlsec-1.2.1-gt4.jar
|   |   |   |   `-- xwork-core-2.2.1.jar
|   |   |   |-- sitemesh.xml
|   |   |   |-- tiles.xml
|   |   |   |-- tld
|   |   |   |   |-- c.tld
|   |   |   |   `-- tiles-jsp.tld
|   |   |   `-- web.xml
|   |   |-- css
|   |   |   |-- blueprint
|   |   |   |   |-- ie.css
|   |   |   |   |-- plugins
|   |   |   |   |   `-- fancy-type
|   |   |   |   |       |-- readme.txt
|   |   |   |   |       `-- screen.css
|   |   |   |   |-- print.css
|   |   |   |   |-- screen.css
|   |   |   |   `-- src
|   |   |   |       |-- forms.css
|   |   |   |       |-- grid.css
|   |   |   |       |-- grid.png
|   |   |   |       |-- ie.css
|   |   |   |       |-- print.css
|   |   |   |       |-- reset.css
|   |   |   |       `-- typography.css
|   |   |   |-- cipres.css
|   |   |   |-- custom.css
|   |   |   |-- displaytag.css
|   |   |   `-- messages.css
|   |   |-- decorators
|   |   |   |-- default.jsp
|   |   |   `-- simple.jsp
|   |   |-- help
|   |   |   `-- cite.html
|   |   |-- images
|   |   |   |-- Calendar-July21-FINAL.jpg
|   |   |   |-- Poweredbyteragridsmall.jpg
|   |   |   |-- background.gif
|   |   |   |-- banner_nigms.gif
|   |   |   |-- bg_button_a.gif
|   |   |   |-- bg_button_div.gif
|   |   |   |-- button_closed.gif
|   |   |   |-- button_open.gif
|   |   |   |-- chromebg.gif
|   |   |   |-- closed.gif
|   |   |   |-- closed_box.png
|   |   |   |-- closedy2.png
|   |   |   |-- container-bg.gif
|   |   |   |-- database_seq_med.gif
|   |   |   |-- dna_seq_big.gif
|   |   |   |-- dna_seq_med.gif
|   |   |   |-- dna_seq_sm.gif
|   |   |   |-- doubleArrow.gif
|   |   |   |-- doubleArrow_b.gif
|   |   |   |-- doubleArrow_b_dark.gif
|   |   |   |-- doubleArrow_dark.gif
|   |   |   |-- favicon.ico
|   |   |   |-- folder_med.gif
|   |   |   |-- folder_sel_med.gif
|   |   |   |-- folder_sel_sm.gif
|   |   |   |-- folder_sm.gif
|   |   |   |-- footer_b.gif
|   |   |   |-- footer_bg.gif
|   |   |   |-- front_button_a.gif
|   |   |   |-- front_button_div.gif
|   |   |   |-- g_bwservice_tool_med.gif
|   |   |   |-- g_bwservice_tool_sm.gif
|   |   |   |-- headerBullet.gif
|   |   |   |-- ibm.gif
|   |   |   |-- ico_file_csv.png
|   |   |   |-- ico_file_excel.png
|   |   |   |-- ico_file_pdf.png
|   |   |   |-- ico_file_xml.png
|   |   |   |-- iconCalendar.gif
|   |   |   |-- iconEmail.gif
|   |   |   |-- iconHelp.gif
|   |   |   |-- iconInformation.gif
|   |   |   |-- iconWarning.gif
|   |   |   |-- info.png
|   |   |   |-- li-bullet.gif
|   |   |   |-- list.gif
|   |   |   |-- logo.gif
|   |   |   |-- ms_research.gif
|   |   |   |-- navInner_bg.gif
|   |   |   |-- nav_bg.gif
|   |   |   |-- new.gif
|   |   |   |-- newstructure.jpg
|   |   |   |-- off_bg.gif
|   |   |   |-- open.gif
|   |   |   |-- open_box.png
|   |   |   |-- opencq8.png
|   |   |   |-- page-head-bg.gif
|   |   |   |-- page.gif
|   |   |   |-- panel_bg.gif
|   |   |   |-- panel_bg_up.gif
|   |   |   |-- pw-icon.jpg
|   |   |   |-- report_issue_plain.gif
|   |   |   |-- request_feature_plain.gif
|   |   |   |-- results_doc_med.gif
|   |   |   |-- results_doc_sm.gif
|   |   |   |-- return.gif
|   |   |   |-- sample_boxshade_output.gif
|   |   |   |-- sample_form.gif
|   |   |   |-- sample_form_b.gif
|   |   |   |-- sdsc_logo.gif
|   |   |   |-- singleArrow.gif
|   |   |   |-- singleArrow_b.gif
|   |   |   |-- singleArrow_b_dark.gif
|   |   |   |-- singleArrow_dark.gif
|   |   |   |-- subscribe.gif
|   |   |   |-- tab-left-over.gif
|   |   |   |-- tab-left.gif
|   |   |   |-- tab-right-over.gif
|   |   |   |-- tab-right.gif
|   |   |   |-- tabs_left.gif
|   |   |   |-- tabs_left_over.gif
|   |   |   |-- tabs_right.gif
|   |   |   |-- tabs_right_over.gif
|   |   |   |-- tdRow.gif
|   |   |   |-- thRow.gif
|   |   |   |-- traffic-light-all.jpg
|   |   |   |-- ucsd_logo.gif
|   |   |   `-- wrap-bg.gif
|   |   |-- index.html
|   |   |-- index.jsp
|   |   |-- js
|   |   |   |-- animatedcollapse.js
|   |   |   |-- checkboxgroup.js
|   |   |   |-- global.js
|   |   |   |-- need-info.js
|   |   |   |-- ngbw.js
|   |   |   |-- simpletreemenu.js
|   |   |   |-- swami.js
|   |   |   `-- switchcontent.js
|   |   `-- pages
|   |       |-- common
|   |       |   |-- banner.jsp
|   |       |   |-- dataUploadLists.jsp
|   |       |   |-- datasetLists.jsp
|   |       |   |-- footer.jsp
|   |       |   |-- header.jsp
|   |       |   |-- loginBox.jsp
|   |       |   |-- menu.jsp
|   |       |   |-- messages-updated.jsp
|   |       |   |-- messages.jsp
|   |       |   |-- meta.jsp
|   |       |   |-- taglibs.jsp
|   |       |   `-- underconstruction.jsp
|   |       |-- default
|   |       |   |-- content.jsp
|   |       |   `-- navigation.jsp
|   |       |-- layouts
|   |       |   |-- forward.jsp
|   |       |   |-- mainLayout.jsp
|   |       |   |-- popupLayout.jsp
|   |       |   `-- popupLayoutEx.jsp
|   |       |-- static
|   |       |   |-- compatibility.jsp
|   |       |   |-- contact.jsp
|   |       |   |-- error.html
|   |       |   |-- faq.jsp
|   |       |   |-- funding.jsp
|   |       |   |-- help.jsp
|   |       |   |-- home.html
|   |       |   |-- links.jsp
|   |       |   |-- news.jsp
|   |       |   |-- publications.jsp
|   |       |   |-- tool
|   |       |   |   |-- blast2.html
|   |       |   |   |-- boxshade.html
|   |       |   |   |-- clique.html
|   |       |   |   |-- clustalw.html
|   |       |   |   |-- consense.html
|   |       |   |   |-- dnadist.html
|   |       |   |   |-- dnapars.html
|   |       |   |   |-- dollop.html
|   |       |   |   |-- mfold.html
|   |       |   |   |-- mix.html
|   |       |   |   |-- pars.html
|   |       |   |   |-- perl.pl
|   |       |   |   |-- protdist.html
|   |       |   |   |-- protpars.html
|   |       |   |   |-- psiblast.html
|   |       |   |   |-- seqboot.html
|   |       |   |   |-- tool_tests
|   |       |   |   |   |-- align_nuc_out1.txt
|   |       |   |   |   |-- alignn1_in.txt
|   |       |   |   |   |-- alignn2_in.txt
|   |       |   |   |   |-- blast2seqn1_in.txt
|   |       |   |   |   |-- blast2seqn2_in.txt
|   |       |   |   |   |-- blast2seqn_out1.txt
|   |       |   |   |   |-- blimps_in.txt
|   |       |   |   |   |-- blimps_out.txt
|   |       |   |   |   |-- clustal_profile_test_in1.aln
|   |       |   |   |   |-- clustal_profile_test_in2.aln
|   |       |   |   |   |-- clustal_profile_test_out1.aln
|   |       |   |   |   |-- clustal_seq_in.fasta
|   |       |   |   |   |-- clustal_test1.txt
|   |       |   |   |   |-- clustal_test1_out1.txt
|   |       |   |   |   |-- clustal_test_out2.txt
|   |       |   |   |   |-- clustalw_tree_in1.aln
|   |       |   |   |   |-- clustalw_tree_out1.ph
|   |       |   |   |   |-- clustalwdist_test_in_1.aln
|   |       |   |   |   |-- clustalwdist_test_out1.dst.txt
|   |       |   |   |   |-- clustalwdist_test_out1.ph.txt
|   |       |   |   |   |-- degapseqn_in.txt
|   |       |   |   |   |-- degapseqn_out.txt
|   |       |   |   |   |-- fastx_in.txt
|   |       |   |   |   |-- fastx_out.txt
|   |       |   |   |   |-- fasty_in.txt
|   |       |   |   |   |-- fasty_out.txt
|   |       |   |   |   |-- fingerprintscan_in.txt
|   |       |   |   |   |-- fingerprintscan_test_out1.txt
|   |       |   |   |   |-- hmmpfam_in.txt
|   |       |   |   |   |-- hmmpfam_out1.txt
|   |       |   |   |   |-- hth_input1.txt
|   |       |   |   |   |-- hth_output1.txt
|   |       |   |   |   |-- lalign1_in.txt
|   |       |   |   |   |-- lalign2_in.txt
|   |       |   |   |   |-- lalign_out1.txt
|   |       |   |   |   |-- mfoldtest1.pdf
|   |       |   |   |   |-- mfoldtest2.pdf
|   |       |   |   |   |-- mview.html
|   |       |   |   |   |-- mviewalign_in1.txt
|   |       |   |   |   |-- mviewalign_out1.html
|   |       |   |   |   |-- mviewblast_in1.txt
|   |       |   |   |   |-- mviewblast_out1.html
|   |       |   |   |   |-- pepinfo_in.txt
|   |       |   |   |   |-- pepstats_in.txt
|   |       |   |   |   |-- pepstats_out.txt
|   |       |   |   |   |-- pepwndow_in1.txt
|   |       |   |   |   |-- pfscan_in.txt
|   |       |   |   |   |-- pfscan_out.txt
|   |       |   |   |   |-- pfsearch_profile_in.txt
|   |       |   |   |   |-- phyml_input1.txt
|   |       |   |   |   |-- phyml_output_stats.txt
|   |       |   |   |   |-- phyml_output_trees.txt
|   |       |   |   |   |-- ppsearch_in.txt
|   |       |   |   |   |-- ppsearch_out.txt
|   |       |   |   |   |-- prosearch_in.txt
|   |       |   |   |   |-- prosearch_out.txt
|   |       |   |   |   |-- prss_out1.txt
|   |       |   |   |   |-- prssn1_in.txt
|   |       |   |   |   |-- prssn2_in.txt
|   |       |   |   |   |-- revseq_in.txt
|   |       |   |   |   |-- revseq_out.txt
|   |       |   |   |   |-- rpsblast_in.txt
|   |       |   |   |   |-- rpsblast_out.txt
|   |       |   |   |   |-- sixpack_in.txt
|   |       |   |   |   |-- sixpack_out.txt
|   |       |   |   |   |-- ssearch_in.txt
|   |       |   |   |   |-- ssearch_out.txt
|   |       |   |   |   |-- tacg_in.txt
|   |       |   |   |   |-- tacg_out.txt
|   |       |   |   |   |-- tfasta_in.txt
|   |       |   |   |   |-- tfasta_out1.txt
|   |       |   |   |   |-- tfastx_in.txt
|   |       |   |   |   |-- tfastx_out.txt
|   |       |   |   |   |-- tfasty_in.txt
|   |       |   |   |   |-- tfasty_out.txt
|   |       |   |   |   |-- tmap.1.png
|   |       |   |   |   `-- tmap1.txt
|   |       |   |   `-- unroot.html
|   |       |   `-- unavailable.html
|   |       |-- tool
|   |       |   |-- align.jsp
|   |       |   |-- beast_tg.jsp
|   |       |   |-- bl2seq.jsp
|   |       |   |-- blast2.jsp
|   |       |   |-- blastn.jsp
|   |       |   |-- blastp.jsp
|   |       |   |-- blastx.jsp
|   |       |   |-- blimps.jsp
|   |       |   |-- boxshade.jsp
|   |       |   |-- bucky.jsp
|   |       |   |-- clearcut.jsp
|   |       |   |-- clique.jsp
|   |       |   |-- clustalw.jsp
|   |       |   |-- clustalw_dist.jsp
|   |       |   |-- clustalw_n.jsp
|   |       |   |-- clustalw_p.jsp
|   |       |   |-- clustalw_profile.jsp
|   |       |   |-- clustalw_tree.jsp
|   |       |   |-- compass.jsp
|   |       |   |-- consense.jsp
|   |       |   |-- contralign.jsp
|   |       |   |-- degapseq.jsp
|   |       |   |-- dnadist.jsp
|   |       |   |-- dnapars.jsp
|   |       |   |-- dollop.jsp
|   |       |   |-- drawgram.jsp
|   |       |   |-- drawtree.jsp
|   |       |   |-- dssp.jsp
|   |       |   |-- epestfind.jsp
|   |       |   |-- eprimer3.jsp
|   |       |   |-- extractalign.jsp
|   |       |   |-- extractseq.jsp
|   |       |   |-- fasta_n.jsp
|   |       |   |-- fasta_p.jsp
|   |       |   |-- fastx.jsp
|   |       |   |-- fasty.jsp
|   |       |   |-- fingerprintscan.jsp
|   |       |   |-- fitch.jsp
|   |       |   |-- formatvalidator.jsp
|   |       |   |-- fsa.jsp
|   |       |   |-- garli.jsp
|   |       |   |-- garli2_tgb.jsp
|   |       |   |-- garli_abe.jsp
|   |       |   |-- garli_conf_creator.jsp
|   |       |   |-- garli_lonestar.jsp
|   |       |   |-- garli_tg.jsp
|   |       |   |-- helixturnhelix.jsp
|   |       |   |-- hmmpfam.jsp
|   |       |   |-- kitsch.jsp
|   |       |   |-- lalign.jsp
|   |       |   |-- mafft.jsp
|   |       |   |-- mafft_tg.jsp
|   |       |   |-- mafftnew.jsp
|   |       |   |-- mbsum.jsp
|   |       |   |-- merger.jsp
|   |       |   |-- mfold.jsp
|   |       |   |-- mix.jsp
|   |       |   |-- mrbayes.jsp
|   |       |   |-- mrbayes_abe.jsp
|   |       |   |-- mrbayes_lonestar.jsp
|   |       |   |-- mrbayeshybrid_abe.jsp
|   |       |   |-- mrbayeshybrid_tg.jsp
|   |       |   |-- msa.jsp
|   |       |   |-- muscle.jsp
|   |       |   |-- mview_alig.jsp
|   |       |   |-- mview_blast.jsp
|   |       |   |-- nclconverter.jsp
|   |       |   |-- neighbor.jsp
|   |       |   |-- new_tool.jsp
|   |       |   |-- pars.jsp
|   |       |   |-- paup.jsp
|   |       |   |-- pauprat.jsp
|   |       |   |-- pauprat_exp.jsp
|   |       |   |-- pepinfo.jsp
|   |       |   |-- pepstats.jsp
|   |       |   |-- pepwindow.jsp
|   |       |   |-- pfscan.jsp
|   |       |   |-- pfsearch.jsp
|   |       |   |-- phyml.jsp
|   |       |   |-- poy.jsp
|   |       |   |-- poy2.jsp
|   |       |   |-- ppsearch.jsp
|   |       |   |-- probalign.jsp
|   |       |   |-- probcons.jsp
|   |       |   |-- prosearch.jsp
|   |       |   |-- protdist.jsp
|   |       |   |-- proteus.jsp
|   |       |   |-- protpars.jsp
|   |       |   |-- prss.jsp
|   |       |   |-- psiblast.jsp
|   |       |   |-- psipred.jsp
|   |       |   |-- raxmlhpc.jsp
|   |       |   |-- raxmlhpc2.jsp
|   |       |   |-- raxmlhpc2_abe.jsp
|   |       |   |-- raxmlhpc2_abe727.jsp
|   |       |   |-- raxmlhpc2_abe_727.jsp
|   |       |   |-- raxmlhpc2_tg.jsp
|   |       |   |-- raxmlhpc2_tgb.jsp
|   |       |   |-- raxmlhpc2bb.jsp
|   |       |   |-- raxmlhpc_abe.jsp
|   |       |   |-- readseq.jsp
|   |       |   |-- restrict.jsp
|   |       |   |-- revseq.jsp
|   |       |   |-- rid3paup.jsp
|   |       |   |-- rid3raxml.jsp
|   |       |   |-- rpsblast.jsp
|   |       |   |-- saps.jsp
|   |       |   |-- seqboot.jsp
|   |       |   |-- seqretsplit.jsp
|   |       |   |-- sixpack.jsp
|   |       |   |-- sleep.jsp
|   |       |   |-- spidey.jsp
|   |       |   |-- ssearch_n.jsp
|   |       |   |-- ssearch_p.jsp
|   |       |   |-- tacg.jsp
|   |       |   |-- tblastn.jsp
|   |       |   |-- tblastx.jsp
|   |       |   |-- tfasta.jsp
|   |       |   |-- tfastx.jsp
|   |       |   |-- tfasty.jsp
|   |       |   |-- tmap.jsp
|   |       |   `-- unroot.jsp
|   |       `-- user
|   |           |-- data
|   |           |   |-- basicSearch.jsp
|   |           |   |-- dataList.jsp
|   |           |   |-- displayData.jsp
|   |           |   |-- displaySearchResult.jsp
|   |           |   |-- pasteForm.jsp
|   |           |   |-- resultsPage.jsp
|   |           |   |-- searchForm.jsp
|   |           |   |-- treedraw.jsp
|   |           |   `-- uploadForm.jsp
|   |           |-- displayTool.jsp
|   |           |-- folder
|   |           |   |-- displayFolder.jsp
|   |           |   |-- folderForm.jsp
|   |           |   |-- folderList.jsp
|   |           |   `-- importBwbData.jsp
|   |           |-- forgotPassword.jsp
|   |           |-- home.jsp
|   |           |-- login.jsp
|   |           |-- profile.jsp
|   |           |-- register.jsp
|   |           |-- statistics.jsp
|   |           |-- task
|   |           |   |-- displayInput.jsp
|   |           |   |-- displayOutput.jsp
|   |           |   |-- displayOutputList.jsp
|   |           |   |-- displayParameters.jsp
|   |           |   |-- displayTask.jsp
|   |           |   |-- displayTransformedOutput.jsp
|   |           |   |-- displayTransformedRecord.jsp
|   |           |   |-- displayWorkingDirectory.jsp
|   |           |   |-- outputForm.jsp
|   |           |   |-- selectData.jsp
|   |           |   |-- selectTool.jsp
|   |           |   |-- taskForm.jsp
|   |           |   |-- taskList.jsp
|   |           |   `-- taskSummary.jsp
|   |           |-- taskupdateerror.txt
|   |           |-- taskupdateok.txt
|   |           |-- tools.jsp
|   |           |-- updatePassword.jsp
|   |           `-- updateProfile.jsp
|   |-- portal2.war
|   |-- ss_server
|   |   |-- Readme.txt
|   |   |-- log4j-1.2.12.jar
|   |   |-- ss_control
|   |   |-- ss_log4j.xml
|   |   `-- tl2.sh
|   |-- surefire-reports
|   |   |-- TEST-org.ngbw.web.controllers.TestDataFormatController.xml
|   |   |-- TEST-org.ngbw.web.controllers.TestDatasetController.xml
|   |   |-- TEST-org.ngbw.web.controllers.TestFolderController.xml
|   |   |-- TEST-org.ngbw.web.controllers.TestSessionController.xml
|   |   |-- org.ngbw.web.controllers.TestDataFormatController.txt
|   |   |-- org.ngbw.web.controllers.TestDatasetController.txt
|   |   |-- org.ngbw.web.controllers.TestFolderController.txt
|   |   `-- org.ngbw.web.controllers.TestSessionController.txt
|   |-- test-classes
|   |   `-- org
|   |       `-- ngbw
|   |           `-- web
|   |               `-- controllers
|   |                   |-- TestController.class
|   |                   |-- TestDataFormatController.class
|   |                   |-- TestDatasetController.class
|   |                   |-- TestFolderController.class
|   |                   `-- TestSessionController.class
|   `-- war
|       `-- work
|           `-- webapp-cache.xml
`-- tl.sh

125 directories, 2257 files