# ALIGN
#
#
ALIGN.query1_= examples/tooltest/ALIGN/alignn1_in.txt
ALIGN.query2_= examples/tooltest/ALIGN/alignn2_in.txt
#
#
#

# BL2SEQ
#
#
BL2SEQ.first_sequence_= examples/tooltest/BLAST2SEQ/blast2seqn1_in.txt
BL2SEQ.second_sequence_= examples/tooltest/BLAST2SEQ/blast2seqn2_in.txt
#
#
#

# BLAST2
#
#
BLAST2.query_= examples/tooltest/BLAST2/blast2_in.txt
#
#
#

# BLASTN
#
#
BLASTN.query_= examples/tooltest/BLAST2/blastn_in.txt
#
#
#

# BLASTP
#
#
BLASTP.query_= examples/tooltest/BLAST2/blastp_in.txt
#
#
#

# BLASTX
#
#
BLASTX.query_= examples/tooltest/BLAST2/blastx_in.txt
#
#
#

# BLIMPS
#
#
BLIMPS.sequence_file_= examples/tooltest/BLIMPS/blimps_seq_in.txt
#
#
#

# BOXSHADE
#
#
BOXSHADE.alignment_= examples/tooltest/BOXSHADE/boxshadep_in.aln
#
#
#

# CLIQUE
#
#
CLIQUE.infile_= examples/tooltest/CLIQUE/clique_in.phy
#
#
#

# CLUSTALW
#
#
CLUSTALW.infile_= examples/tooltest/CLUSTALW/clustalw_seq_in.fasta
#
#
#

# CLUSTALW_DIST
#
#
CLUSTALW_DIST.infile_= examples/tooltest/CLUSTALW/clustalw_dist_in.txt
#
#
#

# CLUSTALW_PROFILE
#
#

CLUSTALW_PROFILE.profile1_=examples/tooltest/CLUSTALW/clustal_profile1profileseq_1.aln
CLUSTALW_PROFILE.profile2_=examples/tooltest/CLUSTALW/clustal_profile2profileseq_2.aln
CLUSTALW_PROFILE.usetree1_=examples/tooltest/CLUSTALW/clustalw_seq_in_guidetree.dnd
CLUSTALW_PROFILE.usetree2_=examples/tooltest/CLUSTALW/clustalw_tree_in.dnd
#
#
#

# CLUSTALW_TREE
#
#
CLUSTALW_TREE.infile_= examples/tooltest/CLUSTALW/clustal_tree_in.aln
#
#
#

# CONSENSE
#
#
CONSENSE.infile_= examples/tooltest/CONSENSE/consense_in.dnd
#
#
#

# DEGAPSEQ
#
#
DEGAPSEQ.sequence_= examples/tooltest/DEGAPSEQ/degapseq_in.txt
#
#
#

# DNADIST
#
#
DNADIST.infile_= examples/tooltest/DNADIST/dnadist_in.phy
#
#
#

# DNAPARS
#
#
DNAPARS.infile_= examples/tooltest/DNAPARS/dnapars_in.phy
#
#
#

# DOLLOP
#
#
DOLLOP.infile_= examples/tooltest/DOLLOP/dollop_in.phy
DOLLOP.tree_file_= examples/tooltest/DOLLOP/dollop_in_guidetree.dnd
#
#
#

# DRAWGRAM
#
#
DRAWGRAM.treefile_= examples/tooltest/DRAWGRAM/drawgram_in.dnd
#
#
#

# DRAWTREE
#
#
DRAWTREE.treefile_= examples/tooltest/DRAWTREE/drawtree_in.dnd
#
#
#

# DSSP
#
#
DSSP.pdbfile_= examples/tooltest/DSSP/dssp_in.pdb
#
#
#

# FASTA_N
#
#
FASTA_N.query_= examples/tooltest/FASTA/fastan_in.txt
#
#
#

# FASTA_P
#
#
FASTA_P.query_= examples/tooltest/FASTA/fastap_in.txt
#
#
#

# FASTAX
#
#
FASTX.query_= examples/tooltest/FASTA/fastx_in.txt
#
#
#

# FASTAY
#
#
FASTY.query_= examples/tooltest/FASTA/fasty_in.txt
#
#
#

# FINGERPRINTSCAN
#
#
FINGERPRINTSCAN.sequence_= examples/tooltest/FINGERPRINTSCAN/fingerprintscan_in.txt
#
#
#

# FITCH
#
#
FITCH.infile_= examples/tooltest/FITCH/fitch_in.pdm
#
#
#

# GARLI
#
#
GARLI.infile_= examples/tooltest/GARLI/GARLI_in.txt

# uncomment/comment out  these two to test with/without a starting tree and topology constraint file.
GARLI.streefname_userdata_=examples/tooltest/GARLI/small.tre
GARLI.constraintfile_control_=examples/tooltest/GARLI/constraint.txt
#
#
#


# HELIXTURNHELIX
#
#
HELIXTURNHELIX.sequence_= examples/tooltest/HELIXTURNHELIX/helixturnhelix_in.txt
#
#
#

# HMMPFAM
#
#
HMMPFAM.seqfile_= examples/tooltest/HMMPFAM/hmmpfam_in.txt
#
#
#

# KITSCH
#
#
KITSCH.infile_= examples/tooltest/KITSCH/kitsch_in.pdm
#
#
#

# LALIGN
#
#
LALIGN.query1_= examples/tooltest/LALIGN/lalign1_in.txt
LALIGN.query2_= examples/tooltest/LALIGN/lalign2_in.txt
#
#
#

# MAFFT
#
#
MAFFT.infile_= examples/tooltest/MAFFT/MAFFT_in.txt
#
#
#

# MFOLD
#
#
MFOLD.SEQ_= examples/tooltest/MFOLD/mfold_in.txt
#
#
#

# MIX
#
#
MIX.infile_= examples/tooltest/MIX/mix_in.phy
MIX.mixture_file_= examples/tooltest/MIX/mixture.txt
MIX.tree_file_= examples/tooltest/MIX/mix_usertree.txt
#
#
#

# MSA
#
#
MSA.seqs_= examples/tooltest/MSA/msa_nucl_in.txt
#
#
#

# MVIEW_ALIG
#
#
MVIEW_ALIG.alig_= examples/tooltest/MVIEW_ALIG/mview_alig_in.txt
#
#
#

# MVIEW_BLAST
#
#
MVIEW_BLAST.blast_output_= examples/tooltest/MVIEW_BLAST/mview_blast_in.txt
#
#
#

# NEIGHBOR
#
#
NEIGHBOR.infile_= examples/tooltest/NEIGHBOR/neighbor_in.pdm
#
#
#

# PARS
#
#
PARS.infile_= examples/tooltest/PARS/pars_in.phy
#
#
#

# PEPINFO
#
#
PEPINFO.sequence_= examples/tooltest/PEPINFO/pepinfo_in.txt
#
#
#

# PEPSTATS
#
#
PEPSTATS.sequence_= examples/tooltest/PEPSTATS/pepstats_in.txt
#
#
#

# PEPWINDOW
#
#
PEPWINDOW.sequence_= examples/tooltest/PEPWINDOW/pepwindow_in.txt
#
#
#

# PFSCAN
#
#
PFSCAN.seqfile_= examples/tooltest/PFSCAN/pfscan_in.txt
#
#
#

# PFSEARCH
#
#
PFSEARCH.profile_= examples/tooltest/PFSEARCH/pfsearch_matrix_in.txt
#
#
#

# PHYML
#
#
PHYML.alignment_= examples/tooltest/PHYML/phyml_in.aln
PHYML.user_tree_file_= examples/tooltest/PHYML/phyml_guidetree.dnd
#
#
#

# PPSEARCH
#
#
PPSEARCH.inputfile_= examples/tooltest/PPSEARCH/ppsearch_in.txt
#
#
#

# PROBALIGN
#
#
PROBALIGN.infile_= examples/tooltest/PROBALIGN/PROBALIGN_in.txt
#
#
#

# EPRIMER3
#
#
EPRIMER3.sequence_= examples/tooltest/PRIMERS/primers_in.txt
#
#
#

# PROSEARCH
#
#
PROSEARCH.protein_= examples/tooltest/PROSEARCH/prosearch_in.txt
#
#
#

# PROTDIST
#
#
PROTDIST.infile_= examples/tooltest/PROTDIST/protdist_in.phy
#
#
#

# PROTPARS
#
#
PROTPARS.infile_= examples/tooltest/PROTPARS/protpars_in.phy
#
#
#


# PROTEUS
#
#
# PROTEUS.sequence_= examples/tooltest/PROTEUS/proteus_in.fasta
#
#
#

# PRSS
#
#
PRSS.query1_= examples/tooltest/PRSS/prssn1_in.txt
PRSS.query2_= examples/tooltest/PRSS/prssn2_in.txt
#
#
#

# PSIBLAST
#
#
PSIBLAST.query_= examples/tooltest/PSIBLAST/psiblast_in.txt
#
#
#

# PSIPRED
#
#
PSIPRED.sequence_= examples/tooltest/PSIPRED/psipred_in.txt
#
#
#

# RAXMLHPC
#
#
RAXMLHPC.infile_= examples/tooltest/RAXMLHPC/RAXMLHPC_in.txt
#
#
#


# REVSEQ
#
#
REVSEQ.sequence_= examples/tooltest/REVSEQ/revseq_in.txt
#
#
#

# RPSBLAST
#
#
RPSBLAST.query_= examples/tooltest/RPSBLAST/rpsblast_in.txt
#
#
#

# SAPS
#
#
SAPS.seq_= examples/tooltest/SAPS/saps_in.txt
#
#
#

# SEQBOOT
#
#
SEQBOOT.infile_= examples/tooltest/SEQBOOT/seqboot_in.txt
#
#
#

# SIXPACK
#
#
SIXPACK.sequence_= examples/tooltest/SIXPACK/sixpack_in.txt
#
#
#

# SSEARCH_P
#
#
SSEARCH_P.query_= examples/tooltest/SSEARCH/ssearch_in1.txt
#
#
#

# SSEARCH_N
#
#
SSEARCH_N.query_= examples/tooltest/SSEARCH/ssearch_in2.txt
#
#
#


# TACG
#
#
TACG.sequence_= examples/tooltest/TACG/tacg_in.txt
#
#
#

# TBLASTN
#
#
TBLASTN.query_= examples/tooltest/BLAST2/tblastn_in.txt
#
#
#

# TBLASTX
#
#
TBLASTX.query_= examples/tooltest/BLAST2/tblastx_in.txt
#
#
#

# TFASTA
#
#
TFASTA.query_= examples/tooltest/FASTA/tfasta_in.txt
#
#
#

# TFASTAX
#
#
TFASTX.query_= examples/tooltest/FASTA/tfastx_in.txt
#
#
#

# TFASTAY
#
#
TFASTY.query_= examples/tooltest/FASTA/tfasty_in.txt
#
#
#

# TMAP
#
#
TMAP.sequences_= examples/tooltest/TMAP/tmap_in.aln
#
#
#

# UNROOT
#
#
UNROOT.treefile_= examples/tooltest/UNROOT/unroot_clustal_in.dnd
#
#
#