#
# When you make changes to anything in the sdk, you can use this file
# and the ToolTest class to make sure you haven't broken any tools
# that were running.  Therefore, everything in here *must* run:
# if you add parameters for a tool you are testing and you aren't
# finished, or it doesn't work, please comment them out before
# committing this file.  Also be sure to add any required entries
# in testInputFiles.properties and the corresponding tool data dir.
#
# Tests that are *slow*, for example, that won't complete in 15 min
# or less, should be added to the end of this file, after the
# "These are Slow tools" comment.  That way, we can easily run just
# the "fast" tests when we want to by creating a temporary version
# of this file and removing or commenting out the slow tests.
#

# New PiseCommandRenderer Problem with Clique check the other ones

# ALIGN (exit value not 0)
#
#
#ALIGN.matrix_=BL50
#ALIGN.linlen_=60
#
#
#

# MSA (exit value not 0)
#
#
#MSA.optimal_=0
#MSA.endgap_=0
#MSA.unweight_=0
#
#
#


# PHYML (exit value not 0)
#
#
#PHYML.data_type_=0
#PHYML.datasets_=1
#PHYML.bootstrap_sets_=2
#PHYML.model_=HKY
#PHYML.kappa_=4
#PHYML.kappa_e_=1
#PHYML.invar_=0.0
#PHYML.invar_e_=1
#PHYML.nb_categ_=1
#PHYML.alpha_=1.0
#PHYML.alpha_e_=1
#PHYML.opt_topology_=1
#PHYML.opt_lengths_=1
#
#
#

# SAPS (exit value not 0)
#
#
#SAPS.documented_=0
#SAPS.terse_=0
#SAPS.verbose_=0
#SAPS.table_=0
#SAPS.specie_=swp23s
#SAPS.H_positive_=0
#
#
#


# BL2SEQ
#
#
BL2SEQ.bl2seq_=blastp
BL2SEQ.Expect_=10.0
BL2SEQ.filter_=1
BL2SEQ.lower_case_=0
BL2SEQ.word_size_=0
BL2SEQ.gapped_alig_=1
BL2SEQ.matrix_=BLOSUM62
BL2SEQ.mismatch_=-3
BL2SEQ.match_=1
BL2SEQ.strand_=3
BL2SEQ.dbsize_=0
BL2SEQ.searchspacesize_=0
BL2SEQ.outformat_=0
#
#
#

# BLAST2
#
#
BLAST2.blast2_=blastp
BLAST2.protein_db_=UNIPROT
BLAST2.nucleotid_db_=GBMAM
BLAST2.filter_=1
BLAST2.lower_case_=0
BLAST2.Expect_=10
BLAST2.gapped_alig_=1
BLAST2.mismatch_=-3
BLAST2.match_=1
BLAST2.matrix_=BLOSUM62
BLAST2.gc_query_=1
BLAST2.gc_db_=1
BLAST2.strand_=3
BLAST2.Descriptions_=500
BLAST2.Alignments_=250
BLAST2.view_alignments_=0
BLAST2.show_gi_=0
BLAST2.believe_=0
BLAST2.htmloutput_=1
BLAST2.external_links_=0
BLAST2.one_HSP_per_line_=0
BLAST2.image_query_=0
#
#
#

# BLASTN
#
#
BLASTN.blast2_=blastn
BLASTN.protein_db_=UNIPROT
BLASTN.nucleotid_db_=GBMAM
BLASTN.filter_=1
BLASTN.lower_case_=0
BLASTN.Expect_=10
BLASTN.gapped_alig_=1
BLASTN.mismatch_=-3
BLASTN.match_=1
BLASTN.matrix_=BLOSUM62
BLASTN.gc_query_=1
BLASTN.gc_db_=1
BLASTN.strand_=3
BLASTN.Descriptions_=500
BLASTN.Alignments_=250
BLASTN.view_alignments_=0
BLASTN.show_gi_=0
BLASTN.believe_=0
BLASTN.htmloutput_=1
BLASTN.external_links_=0
BLASTN.one_HSP_per_line_=0
BLASTN.image_query_=0
#
#
#

# BLASTP
#
#
BLASTP.blast2_=blastp
BLASTP.protein_db_=UNIPROT
BLASTP.nucleotid_db_=GBMAM
BLASTP.filter_=1
BLASTP.lower_case_=0
BLASTP.Expect_=10
BLASTP.gapped_alig_=1
BLASTP.mismatch_=-3
BLASTP.match_=1
BLASTP.matrix_=BLOSUM62
BLASTP.gc_query_=1
BLASTP.gc_db_=1
BLASTP.strand_=3
BLASTP.Descriptions_=500
BLASTP.Alignments_=250
BLASTP.view_alignments_=0
BLASTP.show_gi_=0
BLASTP.believe_=0
BLASTP.htmloutput_=1
BLASTP.external_links_=0
BLASTP.one_HSP_per_line_=0
BLASTP.image_query_=0
#
#
#

# BLASTX
#
#
BLASTX.blast2_=blastx
BLASTX.protein_db_=UNIPROT
BLASTX.nucleotid_db_=GBMAM
BLASTX.filter_=1
BLASTX.lower_case_=0
BLASTX.Expect_=10
BLASTX.gapped_alig_=1
BLASTX.mismatch_=-3
BLASTX.match_=1
BLASTX.matrix_=BLOSUM62
BLASTX.gc_query_=1
BLASTX.gc_db_=1
BLASTX.strand_=3
BLASTX.Descriptions_=500
BLASTX.Alignments_=250
BLASTX.view_alignments_=0
BLASTX.show_gi_=0
BLASTX.believe_=0
BLASTX.htmloutput_=1
BLASTX.external_links_=0
BLASTX.one_HSP_per_line_=0
BLASTX.image_query_=0
# 
#
#

# BLIMPS
#
#
BLIMPS.action_=block
BLIMPS.blocks_db_=blocks.dat
BLIMPS.sequence_db_=UNIPROT.fasta
BLIMPS.conversion_=2
BLIMPS.genetic_code_=0
BLIMPS.strand_=1
BLIMPS.outfile_=blimps.results
BLIMPS.error_=2
BLIMPS.histogram_=0
BLIMPS.scores_number_=0
BLIMPS.repeats_=1
#
#
#

# BOXSHADE
#
#
BOXSHADE.output_format_=e
BOXSHADE.print_name_=1
BOXSHADE.ruler_=0
BOXSHADE.space_between_name_sequence_=1
BOXSHADE.ignored_gaps_=0
BOXSHADE.sequence_characters_=60
BOXSHADE.lines_=1
BOXSHADE.character_size_=10
BOXSHADE.save_shading_=T
BOXSHADE.rotate_=0
BOXSHADE.label_similar_=1
BOXSHADE.label_identical_=0
BOXSHADE.consensus_=0
BOXSHADE.threshold_=0.50
BOXSHADE.different_background_=W
BOXSHADE.different_foreground_=B
BOXSHADE.identical_background_=B
BOXSHADE.identical_foreground_=W
BOXSHADE.similar_background_=1
BOXSHADE.similar_foreground_=B
BOXSHADE.conserved_background_=1
BOXSHADE.conserved_foreground_=B
BOXSHADE.single_=0
BOXSHADE.seq_no_=1
BOXSHADE.hide_=0
BOXSHADE.show_normal_=0
BOXSHADE.matrix_=0
BOXSHADE.outfile_="boxshade.result"
BOXSHADE.psfile_="boxshade.ps"
BOXSHADE.htmlfile_="boxshade.html"
BOXSHADE.pictfile_="boxshade.pict"
BOXSHADE.matrixfile_="boxshade.matrix"
#
#
#

# CLIQUE
#
#
CLIQUE.spec_min_clique_size_=0
CLIQUE.multiple_dataset_=0
CLIQUE.consense_=0
CLIQUE.print_matrix_=1
CLIQUE.print_tree_=1
CLIQUE.print_treefile_=1
CLIQUE.printdata_=0
CLIQUE.indent_tree_=0
CLIQUE.outgroup_=1
#
#
#


# CLUSTALW
#
#
CLUSTALW.actions_=-align
CLUSTALW.phylip_alig_=0
CLUSTALW.quicktree_=slow
CLUSTALW.matrix_=gonnet
CLUSTALW.dnamatrix_=iub
CLUSTALW.gapopen_=10
CLUSTALW.gapext_=0.20
CLUSTALW.endgaps_=1
CLUSTALW.gapdist_=8
CLUSTALW.pgap_=1
CLUSTALW.hgap_=1
CLUSTALW.maxdiv_=30
CLUSTALW.negative_=0
CLUSTALW.transweight_=0.5
CLUSTALW.ktuple_=1
CLUSTALW.topdiags_=5
CLUSTALW.window_=5
CLUSTALW.pairgap_=3.00
CLUSTALW.pwmatrix_=gonnet
CLUSTALW.pwdnamatrix_=iub
CLUSTALW.pwgapopen_=10.00
CLUSTALW.pwgapext_=0.10
CLUSTALW.kimura_=0
CLUSTALW.tossgaps_=0
CLUSTALW.bootstrap_=1000
CLUSTALW.bootlabels_=node
CLUSTALW.outputtree_=PHYLIP
CLUSTALW.outfile_=outfile.aln
CLUSTALW.output_=
CLUSTALW.outorder_=aligned
CLUSTALW.seqnos_=0
CLUSTALW.nosecstr1_=1
CLUSTALW.nosecstr2_=1
CLUSTALW.helixgap_=4
CLUSTALW.strandgap_=4
CLUSTALW.loopgap_=1
CLUSTALW.terminalgap_=2
CLUSTALW.helixendin_=3
CLUSTALW.helixendout_=0
CLUSTALW.strandendin_=1
CLUSTALW.strandendout_=1
CLUSTALW.secstrout_=STRUCTURE
#
#
#


# CLUSTALW_PROFILE
#
#
CLUSTALW_PROFILE.actions_=-profile
CLUSTALW_PROFILE.phylip_alig_=0
CLUSTALW_PROFILE.quicktree_=slow
CLUSTALW_PROFILE.matrix_=gonnet
CLUSTALW_PROFILE.dnamatrix_=iub
CLUSTALW_PROFILE.gapopen_=10
CLUSTALW_PROFILE.gapext_=0.20
CLUSTALW_PROFILE.endgaps_=1
CLUSTALW_PROFILE.gapdist_=8
CLUSTALW_PROFILE.pgap_=1
CLUSTALW_PROFILE.hgap_=1
CLUSTALW_PROFILE.maxdiv_=30
CLUSTALW_PROFILE.negative_=0
CLUSTALW_PROFILE.transweight_=0.5
CLUSTALW_PROFILE.ktuple_=1
CLUSTALW_PROFILE.topdiags_=5
CLUSTALW_PROFILE.window_=5
CLUSTALW_PROFILE.pairgap_=3.00
CLUSTALW_PROFILE.pwmatrix_=gonnet
CLUSTALW_PROFILE.pwdnamatrix_=iub
CLUSTALW_PROFILE.pwgapopen_=10.00
CLUSTALW_PROFILE.pwgapext_=0.10

CLUSTALW_PROFILE.output_=
CLUSTALW_PROFILE.outorder_=aligned
CLUSTALW_PROFILE.seqnos_=0
CLUSTALW_PROFILE.nosecstr1_=1
CLUSTALW_PROFILE.nosecstr2_=1
CLUSTALW_PROFILE.helixgap_=4
CLUSTALW_PROFILE.strandgap_=4
CLUSTALW_PROFILE.loopgap_=1
CLUSTALW_PROFILE.terminalgap_=2
CLUSTALW_PROFILE.helixendin_=3
CLUSTALW_PROFILE.helixendout_=0
CLUSTALW_PROFILE.strandendin_=1
CLUSTALW_PROFILE.strandendout_=1
CLUSTALW_PROFILE.secstrout_=STRUCTURE
#
#
#

# CONSENSE
#
#
CONSENSE.type_=MRE
CONSENSE.print_tree_=1
CONSENSE.print_treefile_=1
CONSENSE.printdata_=0
CONSENSE.indent_tree_=0
CONSENSE.outgroup_=1
CONSENSE.rooted_=0
#
#
#

# DEGAPSEQ
#
#
DEGAPSEQ.outseq_=outseq.out
DEGAPSEQ.outseq_sformat_=fasta
#
#
#

# DNADIST
#
#
DNADIST.distance_=F84
DNADIST.ratio_=2.0
DNADIST.gamma_=0
DNADIST.empirical_frequencies_=1
DNADIST.one_category_=1
DNADIST.seqboot_=0
DNADIST.method_=bootstrap
DNADIST.replicates_=100
DNADIST.matrix_form_=0
DNADIST.printdata_=0
#
#
#

# DNAPARS
#
#
DNAPARS.use_threshold_=0
DNAPARS.use_transversion_=0
DNAPARS.seqboot_=0
DNAPARS.method_=bootstrap
DNAPARS.replicates_=100
DNAPARS.consense_=0
DNAPARS.jumble_=0
DNAPARS.times_=1
DNAPARS.user_tree_=0
DNAPARS.print_tree_=1
DNAPARS.print_steps_=0
DNAPARS.print_sequences_=0
DNAPARS.print_treefile_=1
DNAPARS.printdata_=0
DNAPARS.indent_tree_=0
DNAPARS.outgroup_=1
#
#
#

# DOLLOP
#
#
DOLLOP.dollop_method_=0
DOLLOP.jumble_=0
DOLLOP.times_=1
DOLLOP.user_tree_=0
DOLLOP.multiple_dataset_=0
DOLLOP.print_tree_=1
DOLLOP.print_step_=0
DOLLOP.print_states_=0
DOLLOP.print_treefile_=1
DOLLOP.printdata_=0
DOLLOP.indent_tree_=0
DOLLOP.use_threshold_=0
#
#
#

# DRAWGRAM
#
#
DRAWGRAM.plotter_=L
DRAWGRAM.xres_=500.00
DRAWGRAM.yres_=500.00
DRAWGRAM.laserjet_resolution_=3
DRAWGRAM.pcx_resolution_=3
DRAWGRAM.grows_=Horizontally
DRAWGRAM.tree_style_=C
DRAWGRAM.branch_lengths_=1
DRAWGRAM.horizontal_margins_=1.65
DRAWGRAM.vertical_margins_=2.16
DRAWGRAM.depth_=1.00
DRAWGRAM.stem_=0.05
DRAWGRAM.character_height_=0.3333
DRAWGRAM.ancestral_=I
DRAWGRAM.font_=Hershey
#
#
#

# DRAWTREE
#
#
DRAWTREE.plotter_=L
DRAWTREE.xxres_=500.00
DRAWTREE.xyres_=500.00
DRAWTREE.laserjet_resolution_=3
DRAWTREE.pcx_resolution_=3
DRAWTREE.branch_lengths_=1
DRAWTREE.angle_=M
DRAWTREE.fixed_angle_=0.0
DRAWTREE.rotation_=0.0
DRAWTREE.arc_=0.0
DRAWTREE.iterate_=E
DRAWTREE.horizontal_margins_=1.73
DRAWTREE.vertical_margins_=2.24
DRAWTREE.character_height_=0.3333
DRAWTREE.font_=Hershey
#
#
#

# DSSP
#
#
DSSP.surface_=0
DSSP.classic_=0
#
#
#


# EPRIMER3
#
#
EPRIMER3.minsize_=18
EPRIMER3.maxsize_=27
EPRIMER3.maxdifftm_=100.0
EPRIMER3.explainflag_=0
EPRIMER3.numreturn_=5
EPRIMER3.outfile_=outfile.out
#
#
#

# FINGERPRINTSCAN
#
#
FINGERPRINTSCAN.graph_scan_=0
FINGERPRINTSCAN.number_bits_=
FINGERPRINTSCAN.random_shuffle_=0
FINGERPRINTSCAN.profile_score_=15
#
#
#

# FITCH
#
#
FITCH.method_=FM
FITCH.negative_branch_=0
FITCH.power_=2
FITCH.jumble_=0
FITCH.times_=1
FITCH.multiple_dataset_=0
FITCH.consense_=0
FITCH.user_tree_=0
FITCH.use_lengths_=0
FITCH.print_tree_=1
FITCH.print_treefile_=1
FITCH.printdata_=0
FITCH.indent_tree_=0
FITCH.outgroup_=1
FITCH.triangular_=square
FITCH.global_=0
#
#
#


# HELIXTURNHELIX
#
#
HELIXTURNHELIX.mean_=238.71
HELIXTURNHELIX.sd_=293.61
HELIXTURNHELIX.minsd_=2.5
HELIXTURNHELIX.outfile_=outfile.out
#
#
#


# HMMPFAM
#
#
HMMPFAM.HMMDB_=Pfam_ls
HMMPFAM.E_value_cutoff_=10.0
#
#
#

# KITSCH
#
#
KITSCH.method_=F
KITSCH.negative_branch_=0
KITSCH.power_=2
KITSCH.jumble_=0
KITSCH.times_=1
KITSCH.multiple_dataset_=0
KITSCH.consense_=0
KITSCH.user_tree_=0
KITSCH.print_tree_=1
KITSCH.print_treefile_=1
KITSCH.printdata_=0
KITSCH.indent_tree_=1
KITSCH.triangular_=square
#
#
#


# LALIGN
#
#
LALIGN.matrix_=BL50
LALIGN.linlen_=60
#
#
#


# MAFFT
#
#
MAFFT.executable_=mafft
MAFFT.distanceMetric_=0
MAFFT.weighting_factor_=2.7
MAFFT.retrees_=2
MAFFT.iterativeRefinements_=0
MAFFT.useFFT_=1
MAFFT.noScore_=1
MAFFT.memSave_=0
MAFFT.usePartTree_=0
MAFFT.partTreeMetric_=0
MAFFT.partTreePartitions_=50
MAFFT.opPenaltyGroupToGroup_=1.53
MAFFT.extendPenaltyGroupToGroup_=0.123
MAFFT.opPenaltyPairwise_=-2.00
MAFFT.offsetValuePairwise_=0.1
MAFFT.extendPenaltyPairwise_=-0.1
MAFFT.opPenaltySkip_=-6.00
MAFFT.extendPenaltySkip_=0.00
MAFFT.aaMatrix_=0
MAFFT.blosum_=62
MAFFT.fmodel_=0
MAFFT.outputFormat_=0
MAFFT.outputOrder_=0
MAFFT.outputGuideTree_=0
MAFFT.inputType_=0
#
#
#


# MFOLD
#
#
MFOLD.LC_=linear
MFOLD.NA_=RNA
MFOLD.T_=37
MFOLD.P_=5
MFOLD.NA_CONC_=1.0
MFOLD.MG_CONC_=0.0
MFOLD.MAX_=50
MFOLD.ANN_=none
MFOLD.MODE_=auto
MFOLD.ROT_ANG_=0
MFOLD.START_=1
#
#
#


# MIX
#
#
MIX.use_mixed_=0
MIX.parsimony_method_=neighbor
MIX.jumble_=0
MIX.times_=1
MIX.user_tree_=0
MIX.multiple_dataset_=0
MIX.consense_=0
MIX.print_tree_=1
MIX.print_step_=0
MIX.print_states_=0
MIX.print_treefile_=1
MIX.printdata_=0
MIX.indent_tree_=0
MIX.use_threshold_=0
MIX.outgroup_=1
#
#
#


# MVIEW_ALIG
#
#
MVIEW_ALIG.in_=clustal
MVIEW_ALIG.alignment_=1
MVIEW_ALIG.dna_=0
MVIEW_ALIG.threshold_=70.0
MVIEW_ALIG.ignore_=none
MVIEW_ALIG.con_threshold_=100,90,80,70
MVIEW_ALIG.con_ignore_=none
MVIEW_ALIG.con_gaps_=1
MVIEW_ALIG.maxident_=100
MVIEW_ALIG.html_output_=full
MVIEW_ALIG.textcolor_=black
MVIEW_ALIG.linkcolor_=blue
MVIEW_ALIG.alinkcolor_=red
MVIEW_ALIG.vlinkcolor_=purple
MVIEW_ALIG.css_=off
MVIEW_ALIG.out_=html
#
#
#


# MVIEW_BLAST
#
#
MVIEW_BLAST.in_=blast
MVIEW_BLAST.alignment_=1
MVIEW_BLAST.dna_=0
MVIEW_BLAST.threshold_=70.0
MVIEW_BLAST.ignore_=none
MVIEW_BLAST.con_threshold_=100,90,80,70
MVIEW_BLAST.con_ignore_=none
MVIEW_BLAST.con_gaps_=1
MVIEW_BLAST.maxident_=100
MVIEW_BLAST.html_output_=full
MVIEW_BLAST.textcolor_=black
MVIEW_BLAST.linkcolor_=blue
MVIEW_BLAST.alinkcolor_=red
MVIEW_BLAST.vlinkcolor_=purple
MVIEW_BLAST.css_=off
MVIEW_BLAST.hsp_=ranked
MVIEW_BLAST.strand_=*
MVIEW_BLAST.fasta_strand_=*
MVIEW_BLAST.out_=html
#
#
#

# NEIGHBOR
#
#
NEIGHBOR.distance_method_=neighbor
NEIGHBOR.jumble_=0
NEIGHBOR.multiple_dataset_=0
NEIGHBOR.consense_=0
NEIGHBOR.print_tree_=1
NEIGHBOR.print_treefile_=1
NEIGHBOR.indent_tree_=0
NEIGHBOR.printdata_=0
NEIGHBOR.outgroup_=1
NEIGHBOR.triangular_=square
#
#
#


# PARS
#
#
PARS.search_opt_=0
PARS.save_trees_=100
PARS.jumble_=0
PARS.times_=1
PARS.user_tree_=0
PARS.multiple_dataset_=0
PARS.multi_times_=1
PARS.consense_=0
PARS.print_tree_=1
PARS.print_step_=0
PARS.print_states_=0
PARS.print_treefile_=1
PARS.printdata_=0
PARS.indent_tree_=0
PARS.use_threshold_=0
PARS.outgroup_=1
#
#
#



# PEPINFO
#
#
PEPINFO.hwindow_=9
PEPINFO.aaproperties_=Eaa_properties.dat
PEPINFO.aahydropathy_=Eaa_hydropathy.dat
PEPINFO.graph_=png
PEPINFO.outfile_=outfile.out
PEPINFO.generalplot_=1
PEPINFO.hydropathyplot_=1
#
#
#


# PEPSTATS
#
#
PEPSTATS.termini_=1
PEPSTATS.aadata_=Eamino.dat
#
#
#


# PEPWINDOW
#
#
PEPWINDOW.length_=7
PEPWINDOW.graph_=png
#
#
#


# PFSCAN
#
#
PFSCAN.pftools_=pfscan
PFSCAN.prosite_=1
#
#
#


# PPSEARCH
#
#
PPSEARCH.abundant_patterns_=0
#
#
#

# PROBALIGN
#
#
PROBALIGN.scoring_matrix_=gonnet_160
PROBALIGN.GapOpen_=22
PROBALIGN.GapExt_=1
PROBALIGN.Temperature_=5
#
# 
#




# PROSEARCH
#
#
#
#
#

# PROTDIST
#
#
PROTDIST.method_=J
PROTDIST.seqboot_=0
PROTDIST.resamp_method_=bootstrap
PROTDIST.replicates_=100
PROTDIST.printdata_=0
PROTDIST.code_=U
PROTDIST.categorization_=G
PROTDIST.change_prob_=0.4570
PROTDIST.ratio_=2.000
#
#
#


# PROTPARS
#
#
PROTPARS.use_threshold_=0
PROTPARS.code_=U
PROTPARS.jumble_=0
PROTPARS.times_=1
PROTPARS.seqboot_=0
PROTPARS.method_=bootstrap
PROTPARS.replicates_=100
PROTPARS.consense_=0
PROTPARS.user_tree_=0
PROTPARS.print_tree_=1
PROTPARS.print_sequences_=0
PROTPARS.print_treefile_=1
PROTPARS.printdata_=0
PROTPARS.print_steps_=0
PROTPARS.indent_tree_=0
PROTPARS.outgroup_=1
#
#
#



# PRSS
#
#
PRSS.matrix_=BL50
#
#
#

# PSIBLAST
#
#
PSIBLAST.start_region_=1
PSIBLAST.end_region_=-1
PSIBLAST.protein_db_=UNIPROT
PSIBLAST.filter_=0
PSIBLAST.Expect_=10
PSIBLAST.window_=40
PSIBLAST.extend_hit_=0
PSIBLAST.dropoff_y_=7.0
PSIBLAST.gapped_alig_=1
PSIBLAST.dropoff_=15
PSIBLAST.dropoff_z_=25
PSIBLAST.matrix_=BLOSUM62
PSIBLAST.open_a_gap_=11
PSIBLAST.extend_a_gap_=1
PSIBLAST.max_passes_=1
PSIBLAST.expect_in_multipass_=0.01
PSIBLAST.pseudocounts_=10
PSIBLAST.trigger_=22.0
PSIBLAST.Descriptions_=500
PSIBLAST.Alignments_=250
PSIBLAST.view_alignments_=0
PSIBLAST.believe_=0
#
#
#




# REVSEQ
#
#
REVSEQ.reverse_=1
REVSEQ.complement_=1
REVSEQ.outseq_=outseq.out
REVSEQ.outseq_sformat_=fasta
#
#
#

# RPSBLAST
#
#
RPSBLAST.protein_db_=Smart
RPSBLAST.Expect_=10.0
RPSBLAST.view_alignments_=0
RPSBLAST.dropoff_y_=7.0
RPSBLAST.dropoff_=15
RPSBLAST.filter_=0
RPSBLAST.trigger_=22.0
RPSBLAST.believe_=0
RPSBLAST.dropoff_z_=25
RPSBLAST.Alignments_=250
RPSBLAST.Descriptions_=500
#
#
#




# SEQBOOT
#
#
SEQBOOT.interleaved_=1
SEQBOOT.data_type_=sequence
SEQBOOT.method_=bootstrap
SEQBOOT.replicates_=100
SEQBOOT.alleles_=0
SEQBOOT.weights_=0
SEQBOOT.categories_=0
SEQBOOT.multiple_weights_=0
SEQBOOT.enzymes_nb_=1
#
#
#

# SIXPACK
#
#
SIXPACK.table_=0
SIXPACK.firstorf_=1
SIXPACK.lastorf_=1
SIXPACK.mstart_=0
SIXPACK.outfile_=outfile.out
SIXPACK.outseq_sformat_=fasta
SIXPACK.reverse_=1
SIXPACK.orfminsize_=1
SIXPACK.number_=1
SIXPACK.width_=60
SIXPACK.length_=0
SIXPACK.margin_=10
SIXPACK.name_=1
SIXPACK.description_=1
SIXPACK.offset_=1
SIXPACK.html_=0
#
#
#

# TACG
#
#
TACG.topology_=1
TACG.degeneracy_=1
TACG.codon_=0
TACG.order_by_cut_=0
TACG.width_=60
TACG.magnitude_=3
TACG.overhang_=1
TACG.summary_=1
TACG.print_fragments_=0
TACG.sites_=0
TACG.translation_frames_=1
TACG.three_letter_=0
TACG.frame_=1
TACG.errors_=0
TACG.name_=pattern1
#
#
#

# TBLASTN
#
#
TBLASTN.blast2_=tblastn
TBLASTN.protein_db_=UNIPROT.fasta
TBLASTN.nucleotid_db_=GBMAM
TBLASTN.filter_=1
TBLASTN.lower_case_=0
TBLASTN.Expect_=10
TBLASTN.gapped_alig_=1
TBLASTN.mismatch_=-3
TBLASTN.match_=1
TBLASTN.matrix_=BLOSUM62
TBLASTN.gc_query_=1
TBLASTN.gc_db_=1
TBLASTN.strand_=3
TBLASTN.Descriptions_=500
TBLASTN.Alignments_=250
TBLASTN.view_alignments_=0
TBLASTN.show_gi_=0
TBLASTN.believe_=0
TBLASTN.htmloutput_=1
TBLASTN.external_links_=0
TBLASTN.one_HSP_per_line_=0
TBLASTN.image_query_=0
#
#
#

# TBLASTX
#
#
TBLASTX.blast2_=tblastx
TBLASTX.protein_db_=UNIPROT.fasta
TBLASTX.nucleotid_db_=GBMAM
TBLASTX.filter_=1
TBLASTX.lower_case_=0
TBLASTX.Expect_=10
TBLASTX.gapped_alig_=1
TBLASTX.mismatch_=-3
TBLASTX.match_=1
TBLASTX.matrix_=BLOSUM62
TBLASTX.gc_query_=1
TBLASTX.gc_db_=1
TBLASTX.strand_=3
TBLASTX.Descriptions_=500
TBLASTX.Alignments_=250
TBLASTX.view_alignments_=0
TBLASTX.show_gi_=0
TBLASTX.believe_=0
TBLASTX.htmloutput_=1
TBLASTX.external_links_=0
TBLASTX.one_HSP_per_line_=0
TBLASTX.image_query_=0
#
#
#


# TMAP
#
#
TMAP.graph_=png
#
#
#

# UNROOT
#
#
#
#
#


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



# GARLI
#
#
GARLI.saveevery_g_=100
GARLI.logevery_g_=10
GARLI.outputeachbettertopology_g_=1
GARLI.inferinternalstateprobs_g_=0
GARLI.outputphyliptree_g_=0
GARLI.outputmostlyuselessfiles_g_=0
GARLI.enforcetermconditions_=1
GARLI.genthreshfortopoterm_=10000
GARLI.significanttopochange_=0.01
GARLI.scorethreshforterm_=0.05
GARLI.stopgen_=214783646
GARLI.stoptime_=214783646
GARLI.bootstrapreps_=0
GARLI.ratematrix_=6rate
GARLI.statefrequencies_=estimate
GARLI.invariantsites_=estimate
GARLI.ratehetmodel_=gamma
GARLI.numratecats_=4
GARLI.refinestart_=1
GARLI.randseed_=-1
GARLI.selectionintensity_=0.5
GARLI.nindivs_=4
GARLI.holdover_=1
GARLI.startoptprec_=0.5
GARLI.minoptprec_=0.01
GARLI.numberofprecreductions_=20
GARLI.modweight_=0.05
GARLI.brlenweight_=0.2
GARLI.randnniweight_=0.1
GARLI.randsprweight_=0.3
GARLI.limsprweight_=0.6
GARLI.limsprrange_=6
GARLI.uniqueswapbias_=0.1
GARLI.writecheckpoints_=0
GARLI.restart_=0
GARLI.holdoverpenalty_=0
GARLI.treerejectionthreshold_=50.0
GARLI.topoweight_=1.0
GARLI.intervallength_=100
GARLI.intervalstostore_=5
GARLI.meanbrlenmuts_=5
GARLI.gammashapebrlen_=1000
GARLI.gammashapemodel_=1000
#
#
#


#
# RAXMLHPC
#
#
RAXMLHPC.datatype_=dna
RAXMLHPC.mlsearch_=0
RAXMLHPC.invariable_=
RAXMLHPC.matrix_=DAYHOFF
RAXMLHPC.empirical_=
RAXMLHPC.bootstop_=auto
RAXMLHPC.bootstrap_seed_=12345
RAXMLHPC.parsimony_seed_=12345
#
#
#



######## These are Slow tools ########

# FASTA_N
#
#
FASTA_N.fasta_=fasta_t
FASTA_N.seqtype_=protein
FASTA_N.protein_db_=UNIPROT.fasta
FASTA_N.nucleotid_db_=GBHTC.fasta
FASTA_N.high_expect_=10.0
FASTA_N.dna_match_=5
FASTA_N.nucleotid_mismatch_=-4
FASTA_N.matrix_=BL50
FASTA_N.genetic_code_=1
FASTA_N.stat_=1
FASTA_N.random_=0
FASTA_N.html_output_=0
FASTA_N.markx_=0
FASTA_N.z_score_out_=0
FASTA_N.linlen_=60
FASTA_N.filter_=0
FASTA_N.html_outfile_="fasta.html"
#
#
#


# FASTA_P
#
#
FASTA_P.fasta_=fasta_t
FASTA_P.seqtype_=protein
FASTA_P.protein_db_=UNIPROT.fasta
FASTA_P.nucleotid_db_=GBHTC.fasta
FASTA_P.high_expect_=10.0
FASTA_P.dna_match_=5
FASTA_P.nucleotid_mismatch_=-4
FASTA_P.matrix_=BL50
FASTA_P.genetic_code_=1
FASTA_P.stat_=1
FASTA_P.random_=0
FASTA_P.html_output_=0
FASTA_P.markx_=0
FASTA_P.z_score_out_=0
FASTA_P.linlen_=60
FASTA_P.filter_=0
FASTA_P.html_outfile_="fasta.html"
#
#
#


# FASTX
#
#
FASTX.fasta_=fastx_t
FASTX.protein_db_=UNIPROT.fasta
FASTX.seqtype_=protein
FASTX.high_expect_=10.0
FASTX.dna_match_=5
FASTX.nucleotid_mismatch_=-4
FASTX.matrix_=BL50
FASTX.genetic_code_=1
FASTX.stat_=1
FASTX.random_=0
FASTX.html_output_=0
FASTX.markx_=0
FASTX.z_score_out_=0
FASTX.linlen_=60
FASTX.filter_=0
FASTX.html_outfile_="fasta.html"
#
#
#
# FASTY
#
#
FASTY.fasta_=fasty_t
FASTY.seqtype_=protein
FASTY.protein_db_=UNIPROT.fasta
FASTY.nucleotid_db_=GBHTC.fasta
FASTY.high_expect_=10.0
FASTY.dna_match_=5
FASTY.nucleotid_mismatch_=-4
FASTY.matrix_=BL50
FASTY.genetic_code_=1
FASTY.stat_=1
FASTY.random_=0
FASTY.html_output_=0
FASTY.markx_=0
FASTY.z_score_out_=0
FASTY.linlen_=60
FASTY.filter_=0
FASTY.html_outfile_="fasta.html"
#
#
#




# SSEARCH_P
#
#
SSEARCH_P.seqtype_=protein
SSEARCH_P.protein_db_=SWISSPROT.fasta
SSEARCH_P.nucleotid_db_=GBHTC.fasta
SSEARCH_P.dna_match_=5
SSEARCH_P.nucleotid_mismatch_=-4
SSEARCH_P.matrix_=BL50
SSEARCH_P.stat_=1
SSEARCH_P.random_=0
SSEARCH_P.html_output_=0
SSEARCH_P.markx_=0
SSEARCH_P.z_score_out_=0
SSEARCH_P.linlen_=60
SSEARCH_P.filter_=0
SSEARCH_P.html_outfile_="ssearch.html"
#
#
#
# SSEARCH_N
#
#
SSEARCH_N.seqtype_=DNA
SSEARCH_N.protein_db_=SWISSPROT.fasta
SSEARCH_N.nucleotid_db_=GBHTC.fasta
SSEARCH_N.dna_match_=5
SSEARCH_N.nucleotid_mismatch_=-4
SSEARCH_N.matrix_=BL50
SSEARCH_N.stat_=1
SSEARCH_N.random_=0
SSEARCH_N.html_output_=0
SSEARCH_N.markx_=0
SSEARCH_N.z_score_out_=0
SSEARCH_N.linlen_=60
SSEARCH_N.filter_=0
SSEARCH_N.html_outfile_="ssearch.html"
#
#
#



# TFASTA
#
#
TFASTA.fasta_=tfasta
TFASTA.seqtype_=protein
TFASTA.protein_db_=UNIPROT.fasta
TFASTA.nucleotid_db_=GBHTC.fasta
TFASTA.high_expect_=10.0
TFASTA.dna_match_=5
TFASTA.nucleotid_mismatch_=-4
TFASTA.matrix_=BL50
TFASTA.genetic_code_=1
TFASTA.stat_=1
TFASTA.random_=0
TFASTA.html_output_=0
TFASTA.markx_=0
TFASTA.z_score_out_=0
TFASTA.linlen_=60
TFASTA.filter_=0
TFASTA.html_outfile_="fasta.html"
#
#
#

# TFASTX
#
#
TFASTX.fasta_=tfastx_t
TFASTX.seqtype_=protein
TFASTX.protein_db_=UNIPROT.fasta
TFASTX.nucleotid_db_=GBHTC.fasta
TFASTX.high_expect_=10.0
TFASTX.dna_match_=5
TFASTX.nucleotid_mismatch_=-4
TFASTX.matrix_=BL50
TFASTX.genetic_code_=1
TFASTX.stat_=1
TFASTX.random_=0
TFASTX.html_output_=0
TFASTX.markx_=0
TFASTX.z_score_out_=0
TFASTX.linlen_=60
TFASTX.filter_=0
TFASTX.html_outfile_="fasta.html"
#
#
#

# TFASTY
#
#
TFASTY.fasta_=tfasty_t
TFASTY.seqtype_=protein
TFASTY.protein_db_=UNIPROT.fasta
TFASTY.nucleotid_db_=GBHTC.fasta
TFASTY.high_expect_=10.0
TFASTY.dna_match_=5
TFASTY.nucleotid_mismatch_=-4
TFASTY.matrix_=BL50
TFASTY.genetic_code_=1
TFASTY.stat_=1
TFASTY.random_=0
#
#
#




#PFSEARCH
#
#
PFSEARCH.pftools_=pfsearch
PFSEARCH.gcg2psa_=0
PFSEARCH.aa_or_nuc_db_=protein
PFSEARCH.aadb_=UNIPROT.fasta
PFSEARCH.nucdb_=genbank
#
#
#