From 4a317845b7f26b5e93bd4d9f5ec350083d3e35b0 Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Fri, 2 Aug 2013 17:18:28 +0100 Subject: [PATCH] Re-format configuration files --- conf/Executable.properties | 5 +- conf/settings/AAConLimits.xml | 53 +++-- conf/settings/AAConParameters.xml | 251 ++++++++++++++++------- conf/settings/AAConPresets.xml | 85 +++++--- conf/settings/ClustalLimits.xml | 33 ++-- conf/settings/ClustalParameters.xml | 14 +- conf/settings/ClustalPresets.xml | 20 +- conf/settings/ClustaloLimits.xml | 20 +- conf/settings/DisemblLimits.xml | 20 +- conf/settings/DisemblParameters.xml | 161 +++++++-------- conf/settings/GlobPlotLimits.xml | 20 +- conf/settings/IUPredLimits.xml | 20 +- conf/settings/IUPredParameters.xml | 14 +- conf/settings/JronnLimits.xml | 20 +- conf/settings/MuscleLimits.xml | 59 +++--- conf/settings/MuscleParameters.xml | 362 +++++++++++++++++++++------------- conf/settings/MusclePresets.xml | 68 ++++--- conf/settings/ProbconsLimits.xml | 22 ++- conf/settings/ProbconsParameters.xml | 25 ++- conf/settings/TcoffeeLimits.xml | 33 ++-- conf/settings/TcoffeeParameters.xml | 2 +- conf/settings/TcoffeePresets.xml | 11 +- 22 files changed, 801 insertions(+), 517 deletions(-) diff --git a/conf/Executable.properties b/conf/Executable.properties index c3d6e52..11a4f24 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -213,7 +213,7 @@ aacon.presets.file = conf/settings/AAConPresets.xml #aacon.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 ########################################################################################### -# MAFFT CONFIGURATION # +# JPRED CONFIGURATION # ########################################################################################### local.jpred.bin = binaries/src/jpred/jpred.pl #cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl @@ -222,5 +222,6 @@ jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast;UNIREFDB#binarie ### This parameters specifies the directory where the matrices files are stored jpred.presets.file = conf/settings/JpredPresets.xml jpred.parameters.file = conf/settings/JpredParameters.xml -#jpred.limits.file = conf/settings/JpredLimits.xml +jpred.limits.file = conf/settings/JpredLimits.xml +jpred.cluster.cpunum = 4 #jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M diff --git a/conf/settings/AAConLimits.xml b/conf/settings/AAConLimits.xml index 5f9a482..6a3b1c2 100644 --- a/conf/settings/AAConLimits.xml +++ b/conf/settings/AAConLimits.xml @@ -1,31 +1,30 @@ - compbio.runner.conservation.AACon - - 5000 - 1000 - - - # LocalEngineExecutionLimit # - 200 - 400 - - - - - Quick conservation - 10000 - 10000 - - - Slow conservation - 2000 - 1000 - - - Complete conservation - 2000 - 1000 - + compbio.runner.conservation.AACon + + 5000 + 1000 + + + # LocalEngineExecutionLimit # + 200 + 400 + + + + Quick conservation + 10000 + 10000 + + + Slow conservation + 2000 + 1000 + + + Complete conservation + 2000 + 1000 + diff --git a/conf/settings/AAConParameters.xml b/conf/settings/AAConParameters.xml index bdc1ef7..5530ebb 100644 --- a/conf/settings/AAConParameters.xml +++ b/conf/settings/AAConParameters.xml @@ -1,74 +1,191 @@ - compbio.runner.conservation.AACon - - Normalize - - Normalize the results. Normalized results have values between 0 and 1. Please note however, - that some results cannot be normalized. In such a case, the system returns not - normalized value. The following formula is used for normalization n = (d - dmin)/(dmax - dmin) - Negative results first converted to positive by adding a greatest absolute result value. - - -n - -n - prog_docs/aacon.txt - - KABAT-m=KABATprog_docs/aacon.txt#KABAT - JORES-m=JORESprog_docs/aacon.txt#JORES - SCHNEIDER-m=SCHNEIDERprog_docs/aacon.txt#SCHNEIDER - SHENKIN-m=SHENKINprog_docs/aacon.txt#SHENKIN-m=SHENKIN - GERSTEIN-m=GERSTEINprog_docs/aacon.txt#GERSTEIN - TAYLOR_GAPS-m=TAYLOR_GAPSprog_docs/aacon.txt#TAYLOR_GAPS - TAYLOR_NO_GAPS-m=TAYLOR_NO_GAPSprog_docs/aacon.txt#TAYLOR_NO_GAPS - ZVELIBIL-m=ZVELIBILprog_docs/aacon.txt#ZVELIBIL - KARLIN-m=KARLINprog_docs/aacon.txt#KARLIN - ARMON-m=ARMONprog_docs/aacon.txt#ARMON - THOMPSON-m=THOMPSONprog_docs/aacon.txt#THOMPSON - NOT_LANCET-m=NOT_LANCETprog_docs/aacon.txt#NOT_LANCET - MIRNY-m=MIRNYprog_docs/aacon.txt#MIRNY - WILLIAMSON-m=WILLIAMSONprog_docs/aacon.txt#WILLIAMSON - LANDGRAF-m=LANDGRAFprog_docs/aacon.txt#LANDGRAF - SANDER-m=SANDERprog_docs/aacon.txt#SANDER - VALDAR-m=VALDARprog_docs/aacon.txt#VALDAR - SMERFS-m=SMERFSprog_docs/aacon.txt#SMERFS - - = - - SMERFS Window Width - The width of the window for SMERFS. Optional, defaults to 7 - -smerfsWW - prog_docs/aacon.txt - 7 - - Integer - 3 - 100 - - - - - SMERFS Column Scoring Method - SMERFS Column Score algorithm defines the window scores to - columns allocation, two methods are possible: MID_SCORE - gives the window score to the middle column - MAX_SCORE - gives the column the highest score of all the windows it belongs to. Optional defaults to MID_SCORE. - -smerfsCS - prog_docs/aacon.txt - MID_SCORE - MAX_SCORE - MID_SCORE - - - - SMERFS Gap Threshhold - a gap percentage cutoff - a float greater than 0 and smaller or equal 1. Optional defaults to 0.1 - -smerfsGT - prog_docs/aacon.txt - 0.1 - - Float + compbio.runner.conservation.AACon + + + Normalize + + Normalize the results. Normalized results have values between 0 and 1. Please note however, + that some results cannot be normalized. In such a case, the system returns not + normalized value. The following formula is used for normalization n = (d - dmin)/(dmax - dmin) + Negative results first converted to positive by adding a greatest absolute result value. + + -n + -n + prog_docs/aacon.txt + + + + SHENKIN + + -m=SHENKIN + prog_docs/aacon.txt#SHENKIN + -m=SHENKIN + + + + KABAT + + -m=KABAT + prog_docs/aacon.txt#KABAT + + + + JORES + + -m=JORES + prog_docs/aacon.txt#JORES + + + + SCHNEIDER + + -m=SCHNEIDER + prog_docs/aacon.txt#SCHNEIDER + + + + GERSTEIN + + -m=GERSTEIN + prog_docs/aacon.txt#GERSTEIN + + + + TAYLOR_GAPS + + -m=TAYLOR_GAPS + prog_docs/aacon.txt#TAYLOR_GAPS + + + + TAYLOR_NO_GAPS + + -m=TAYLOR_NO_GAPS + prog_docs/aacon.txt#TAYLOR_NO_GAPS + + + ZVELIBIL + + -m=ZVELIBIL + prog_docs/aacon.txt#ZVELIBIL + + + + KARLIN + + -m=KARLIN + prog_docs/aacon.txt#KARLIN + + + + ARMON + + -m=ARMON + prog_docs/aacon.txt#ARMON + + + + THOMPSON + + -m=THOMPSON + prog_docs/aacon.txt#THOMPSON + + + + NOT_LANCET + + -m=NOT_LANCET + prog_docs/aacon.txt#NOT_LANCET + + + + MIRNY + + -m=MIRNY + prog_docs/aacon.txt#MIRNY + + + + WILLIAMSON + + -m=WILLIAMSON + prog_docs/aacon.txt#WILLIAMSON + + + LANDGRAF + + -m=LANDGRAF + prog_docs/aacon.txt#LANDGRAF + + + + SANDER + + -m=SANDER + prog_docs/aacon.txt#SANDER + + + + VALDAR + + -m=VALDAR + prog_docs/aacon.txt#VALDAR + + + + SMERFS + + -m=SMERFS + prog_docs/aacon.txt#SMERFS + + + = + + + SMERFS Window Width + + The width of the window for SMERFS. Optional, defaults to 7 + + -smerfsWW + prog_docs/aacon.txt + 7 + + Integer + 3 + 100 + + + + + SMERFS Column Scoring Method + + SMERFS Column Score algorithm defines the window scores to columns allocation, + two methods are possible: MID_SCORE - gives the window score to the middle column + MAX_SCORE - gives the column the highest score of all the windows it belongs to. + Optional defaults to MID_SCORE. + + -smerfsCS + prog_docs/aacon.txt + MID_SCORE + MAX_SCORE + MID_SCORE + + + + SMERFS Gap Threshhold + + a gap percentage cutoff - a float greater than 0 and smaller or equal 1. + Optional defaults to 0.1 + + -smerfsGT + prog_docs/aacon.txt + 0.1 + + Float 0.001 1 - + diff --git a/conf/settings/AAConPresets.xml b/conf/settings/AAConPresets.xml index f2e3cde..721315e 100644 --- a/conf/settings/AAConPresets.xml +++ b/conf/settings/AAConPresets.xml @@ -1,25 +1,66 @@ -compbio.runner.conservation.AACon - - Quick conservation - Collection of fast conservation methods - - - - - - Slow conservation - Collection of most expensive (slow) conservation methods - - - - - - Complete conservation - Calculate conservation with all supported methods - - - - + compbio.runner.conservation.AACon + + Quick conservation + + Collection of fast conservation methods + + + + + + + + + + + + + + + + + + + + Slow conservation + + Collection of most expensive (slow) conservation methods + + + + + + + + + + + + Complete conservation + + Calculate conservation with all supported methods + + + + + + + + + + + + + + + + + + + + + + diff --git a/conf/settings/ClustalLimits.xml b/conf/settings/ClustalLimits.xml index ecb8148..315cb0b 100644 --- a/conf/settings/ClustalLimits.xml +++ b/conf/settings/ClustalLimits.xml @@ -1,21 +1,20 @@ - compbio.runner.clustal.ClustalW - - 1000 - 1000 - - - # LocalEngineExecutionLimit # - 30 - 500 - - - - - Disable gap weighting (Speed-oriented) - 1000 - 3000 - + compbio.runner.msa.ClustalW + + 1000 + 1000 + + + # LocalEngineExecutionLimit # + 30 + 500 + + + + Disable gap weighting (Speed-oriented) + 1000 + 3000 + diff --git a/conf/settings/ClustalParameters.xml b/conf/settings/ClustalParameters.xml index dde49d0..47b1d3f 100644 --- a/conf/settings/ClustalParameters.xml +++ b/conf/settings/ClustalParameters.xml @@ -1,25 +1,30 @@ - compbio.runner.clustal.ClustalW + compbio.runner.msa.ClustalW + NOPGAP Residue-specific gaps off -NOPGAP prog_docs/clustalw.txt + No transition weighting Disable sequence weighting -NOWEIGHTS prog_docs/clustalw.txt + NOHGAP Hydrophilic gaps off -NOHGAP prog_docs/clustalw.txt + = + Transition weighting Type of the sequence (PROTEIN or DNA) @@ -32,6 +37,7 @@ 10 + Type Type of the sequence (PROTEIN or DNA) @@ -41,6 +47,7 @@ PROTEIN DNA + OUTORDER As per INPUT or ALIGNED @@ -49,6 +56,7 @@ INPUT ALIGNED + MATRIX Protein weight matrix @@ -134,6 +142,7 @@ PAM80 PAM90 + GAPOPEN Gap opening penalty @@ -146,6 +155,7 @@ 1000 + -GAPEXT Gap extension penalty @@ -158,6 +168,7 @@ 10 + ENDGAPS End gap separation pen @@ -170,6 +181,7 @@ 10 + GAPDIST Gap separation pen. range diff --git a/conf/settings/ClustalPresets.xml b/conf/settings/ClustalPresets.xml index 3115006..cd067a2 100644 --- a/conf/settings/ClustalPresets.xml +++ b/conf/settings/ClustalPresets.xml @@ -1,13 +1,13 @@ - compbio.runner.clustal.ClustalW - - Disable gap weighting (Speed-oriented) - - - - - - - + compbio.runner.msa.ClustalW + + Disable gap weighting (Speed-oriented) + + + + + + + diff --git a/conf/settings/ClustaloLimits.xml b/conf/settings/ClustaloLimits.xml index 1367ff3..d10037b 100644 --- a/conf/settings/ClustaloLimits.xml +++ b/conf/settings/ClustaloLimits.xml @@ -1,13 +1,13 @@ - compbio.runner.clustal.ClustalO - - 2000 - 1000 - - - # LocalEngineExecutionLimit # - 30 - 500 - + compbio.runner.msa.ClustalO + + 2000 + 1000 + + + # LocalEngineExecutionLimit # + 30 + 500 + diff --git a/conf/settings/DisemblLimits.xml b/conf/settings/DisemblLimits.xml index 914d3b1..0fc3e0c 100644 --- a/conf/settings/DisemblLimits.xml +++ b/conf/settings/DisemblLimits.xml @@ -1,13 +1,13 @@ - compbio.runner.disorder.Disembl - - 5000 - 1000 - - - # LocalEngineExecutionLimit # - 200 - 400 - + compbio.runner.disorder.Disembl + + 5000 + 1000 + + + # LocalEngineExecutionLimit # + 200 + 400 + diff --git a/conf/settings/DisemblParameters.xml b/conf/settings/DisemblParameters.xml index 676395e..c8b7c79 100644 --- a/conf/settings/DisemblParameters.xml +++ b/conf/settings/DisemblParameters.xml @@ -1,88 +1,89 @@ - + + Minimum peak width + Algorithm Parameter: Minimum peak width. + pw + prog_docs/disembl.html + 8 + + Integer + 1 + 30 + + + + + Maximum join distance + Algorithm Parameter: Maximum join distance + jd + prog_docs/disembl.html + 4 + + Integer + 1 + 30 + + + + + Coils threshold + Stringency values for different predictor: Coils threshold + ct + prog_docs/disembl.html + 1.2 + + Float + 0.1 + 10 + + + + + Remark465 threshold + Stringency values for different predictor: Remark465 threshold + rt + prog_docs/disembl.html + 1.4 + + Float + 0.1 + 10 + + + + Hot loops threshold + Stringency values for different predictor: Hot loops threshold. + lt + prog_docs/disembl.html + 1.2 + + Float + 0.1 + 10 + + +--> diff --git a/conf/settings/GlobPlotLimits.xml b/conf/settings/GlobPlotLimits.xml index 7621169..bf31e0f 100644 --- a/conf/settings/GlobPlotLimits.xml +++ b/conf/settings/GlobPlotLimits.xml @@ -1,13 +1,13 @@ - compbio.runner.disorder.GlobPlot - - 5000 - 1000 - - - # LocalEngineExecutionLimit # - 200 - 400 - + compbio.runner.disorder.GlobPlot + + 5000 + 1000 + + + # LocalEngineExecutionLimit # + 200 + 400 + diff --git a/conf/settings/IUPredLimits.xml b/conf/settings/IUPredLimits.xml index 1183c48..73cb41d 100644 --- a/conf/settings/IUPredLimits.xml +++ b/conf/settings/IUPredLimits.xml @@ -1,13 +1,13 @@ - compbio.runner.disorder.IUPred - - 5000 - 1000 - - - # LocalEngineExecutionLimit # - 50 - 400 - + compbio.runner.disorder.IUPred + + 5000 + 1000 + + + # LocalEngineExecutionLimit # + 50 + 400 + diff --git a/conf/settings/IUPredParameters.xml b/conf/settings/IUPredParameters.xml index 5bc99c6..bbdc46d 100644 --- a/conf/settings/IUPredParameters.xml +++ b/conf/settings/IUPredParameters.xml @@ -1,11 +1,15 @@ - compbio.runner.disorder.IUPred - + compbio.runner.disorder.IUPred + + Disorder type - "Long" - for prediction of long disordered regions, "short" - for - prediction of short disordered regions ( e.g. missing residues in - X-ray structures) and "glob" for predicting globular domains. "All" for all methods + + "Long" - for prediction of long disordered regions, "short" - for + prediction of short disordered regions ( e.g. missing residues in + X-ray structures) and "glob" for predicting globular domains. + "All" for all methods + short long glob diff --git a/conf/settings/JronnLimits.xml b/conf/settings/JronnLimits.xml index 9ea48b0..81788ee 100644 --- a/conf/settings/JronnLimits.xml +++ b/conf/settings/JronnLimits.xml @@ -1,13 +1,13 @@ - compbio.runner.disorder.Jronn - - 2000 - 2000 - - - # LocalEngineExecutionLimit # - 5 - 500 - + compbio.runner.disorder.Jronn + + 2000 + 2000 + + + # LocalEngineExecutionLimit # + 5 + 500 + diff --git a/conf/settings/MuscleLimits.xml b/conf/settings/MuscleLimits.xml index b08f536..430968a 100644 --- a/conf/settings/MuscleLimits.xml +++ b/conf/settings/MuscleLimits.xml @@ -1,31 +1,34 @@ - compbio.runner.muscle.Muscle - - 1000 - 1000 - - - # LocalEngineExecutionLimit # - 20 - 500 - - - - - Protein alignment(Fastest speed) - 2000 - 1000 - - - Nucleotide alignment(Fastest speed) - 1000 - 3000 - - - Huge alignments (speed-oriented) - 2000 - 3000 - - + compbio.runner.msa.Muscle + + + 1000 + 1000 + + + + # LocalEngineExecutionLimit # + 20 + 500 + + + + + Protein alignment(Fastest speed) + 2000 + 1000 + + + + Nucleotide alignment(Fastest speed) + 1000 + 3000 + + + + Huge alignments (speed-oriented) + 2000 + 3000 + diff --git a/conf/settings/MuscleParameters.xml b/conf/settings/MuscleParameters.xml index 08ff452..135ca2a 100644 --- a/conf/settings/MuscleParameters.xml +++ b/conf/settings/MuscleParameters.xml @@ -1,7 +1,8 @@ - compbio.runner.muscle.Muscle - - +--> + + + Anchor optimisation - Enable/disable anchor optimization in tree dependent refinement iterations + + Enable/disable anchor optimization in tree dependent refinement iterations + -anchors -noanchors prog_docs/muscle.html -anchors - +--> + Root alignment computation method - Use Steven Brenner's method for computing the root alignment. + + Use Steven Brenner's method for computing the root alignment. + -brenner prog_docs/muscle.html - - +--> + + dimer - Use dimer approximation for the SP score (faster, slightly less accurate) + + Use dimer approximation for the SP score (faster, slightly less accurate) + -dimer prog_docs/muscle.html - + + Diagonal - Use diagonal optimizations. Faster, especially for closely related sequences, but may be less accurate. + + Use diagonal optimizations. Faster, especially for closely related sequences, but may be less accurate. + -diags prog_docs/muscle.html + Diagonal 1 - Use diagonal optimizations in first iteration (faster for similar sequences) + + Use diagonal optimizations in first iteration (faster for similar sequences) + -diags1 prog_docs/muscle.html - + + Profile scoring method - le - use log-expectation profile score VTML240 (default for amino acid sequences.) - sp - use sum-of-pairs protein profile score (PAM200). - sv - use sum-of-pairs profile score (VTML240) + + le - use log-expectation profile score VTML240 (default for amino acid sequences.) + sp - use sum-of-pairs protein profile score (PAM200). + sv - use sum-of-pairs profile score (VTML240) -le -sp -sv prog_docs/muscle.html - -le + -le + - + + Sequence type - Sequence type - Amino acid/Nucleotide + + Sequence type - Amino acid/Nucleotide + -seqtype prog_docs/muscle.html auto @@ -84,19 +109,23 @@ dna rna - + + Maxiters - Maximum number of iterations (integer, default 16) + + Maximum number of iterations (integer, default 16) + -maxiters prog_docs/muscle.html 16 - Integer + Integer 1 100 - +--> + Diagonal break - Maximum distance between two diagonals that allows them to merge into one diagonal + + Maximum distance between two diagonals that allows them to merge into one diagonal + -diagbreak prog_docs/muscle.html 1 - Integer + Integer 1 100 + Diagonal length Minimum length of diagonal @@ -129,223 +162,262 @@ prog_docs/muscle.html 24 - Integer + Integer 2 100 + Diagonal margin - Discard this many positions at ends of diagonal + + Discard this many positions at ends of diagonal + -diagmargin prog_docs/muscle.html 5 - Integer + Integer 1 100 + Anchor spacing - Minimum spacing between anchor columns + + Minimum spacing between anchor columns + -anchorspacing prog_docs/muscle.html 32 - Integer + Integer 2 1000 - + + Matrix - Substitution Matrix to use + + Substitution Matrix to use + -matrix prog_docs/muscle.html BLOSUM62 - BLOSUM100 - BLOSUM30 - BLOSUM35 - BLOSUM40 - BLOSUM45 - BLOSUM50 - BLOSUM55 - BLOSUM60 - BLOSUM62 - BLOSUM65 - BLOSUM70 - BLOSUM75 - BLOSUM80 - BLOSUM85 - BLOSUM90 - BLOSUMN - DAYHOFF - GONNET - IDENTITY - MATCH - NUC.4.2 - NUC.4.4 - PAM10 - PAM100 - PAM110 - PAM120 - PAM130 - PAM140 - PAM150 - PAM160 - PAM170 - PAM180 - PAM190 - PAM20 - PAM200 - PAM210 - PAM220 - PAM230 - PAM240 - PAM250 - PAM260 - PAM270 - PAM280 - PAM290 - PAM30 - PAM300 - PAM310 - PAM320 - PAM330 - PAM340 - PAM350 - PAM360 - PAM370 - PAM380 - PAM390 - PAM40 - PAM400 - PAM410 - PAM420 - PAM430 - PAM440 - PAM450 - PAM460 - PAM470 - PAM480 - PAM490 - PAM50 - PAM500 - PAM60 - PAM70 - PAM80 - PAM90 + BLOSUM100 + BLOSUM30 + BLOSUM35 + BLOSUM40 + BLOSUM45 + BLOSUM50 + BLOSUM55 + BLOSUM60 + BLOSUM62 + BLOSUM65 + BLOSUM70 + BLOSUM75 + BLOSUM80 + BLOSUM85 + BLOSUM90 + BLOSUMN + DAYHOFF + GONNET + IDENTITY + MATCH + NUC.4.2 + NUC.4.4 + PAM10 + PAM100 + PAM110 + PAM120 + PAM130 + PAM140 + PAM150 + PAM160 + PAM170 + PAM180 + PAM190 + PAM20 + PAM200 + PAM210 + PAM220 + PAM230 + PAM240 + PAM250 + PAM260 + PAM270 + PAM280 + PAM290 + PAM30 + PAM300 + PAM310 + PAM320 + PAM330 + PAM340 + PAM350 + PAM360 + PAM370 + PAM380 + PAM390 + PAM40 + PAM400 + PAM410 + PAM420 + PAM430 + PAM440 + PAM450 + PAM460 + PAM470 + PAM480 + PAM490 + PAM50 + PAM500 + PAM60 + PAM70 + PAM80 + PAM90 + Gap open penalty - Gap opening penalty. Must be negative + + Gap opening penalty. Must be negative + -gapopen prog_docs/muscle.html -12.0 - Float + Float -100 0 + Gap extension penalty - Gap extension penalty. Must be negative + + Gap extension penalty. Must be negative + -gapextend prog_docs/muscle.html -1.0 - Float + Float -100 0 + Center - Center parameter. Should be negative. + + Center parameter. Should be negative. + -center prog_docs/muscle.html 0.0 - Float + Float -100 0 + Hydro - Window size for determining whether a region is hydrophobic. + + Window size for determining whether a region is hydrophobic. + -hydro prog_docs/muscle.html 5 - Integer + Integer 0 100 + Hydrofactor - Multiplier for gap open/close penalties in hydrophobic regions. + + Multiplier for gap open/close penalties in hydrophobic regions. + -hydrofactor prog_docs/muscle.html 1.2 - Float + Float 0 10 Minimum anchor score - Minimum score a column must have to be an anchor (default depends on the profile scoring function!) + + Minimum score a column must have to be an anchor + (default depends on the profile scoring function!) + -minbestcolscore prog_docs/muscle.html 1.2 - Float + Float 0 10 + Minimum smoothed anchor score - Minimum smoothed score a column must have to be an anchor (default depends on the profile scoring function!) + + Minimum smoothed score a column must have to be an anchor + (default depends on the profile scoring function!) + -minsmoothscore prog_docs/muscle.html 1.2 - Float + Float 0 10 - + + cluster1 - Clustering method to use on the iteration 1 + + Clustering method to use on the iteration 1 + -cluster1 prog_docs/muscle.html upgma upgma - + + cluster2 - Clustering method to use on the iteration 2 and all subsequent itarations + + Clustering method to use on the iteration 2 and all subsequent itarations + -cluster2 prog_docs/muscle.html upgmb upgmb neighborjoining + Sequence weighting scheme 1 - Sequence weighting scheme to use on the iteration 1 and 2 - none=all sequences have equal weight. - henikoff=Henikoff & Henikoff weighting scheme. - henikoffpb=Modified Henikoff scheme as used in PSI-BLAST. - clustalw=CLUSTALW method. - threeway=Gotoh three-way method + + Sequence weighting scheme to use on the iteration 1 and 2 + none=all sequences have equal weight. + henikoff=Henikoff & Henikoff weighting scheme. + henikoffpb=Modified Henikoff scheme as used in PSI-BLAST. + clustalw=CLUSTALW method. threeway=Gotoh three-way method + -weight1 prog_docs/muscle.html clustalw @@ -356,15 +428,18 @@ clustalw threeway + Sequence weighting scheme 2 - Sequence weighting scheme to use on the iteration 3 and all subsequent - iterations for tree-dependent refinement. - none=all sequences have equal weight. - henikoff=Henikoff & Henikoff weighting scheme. - henikoffpb=Modified Henikoff scheme as used in PSI-BLAST. - clustalw=CLUSTALW method. - threeway=Gotoh three-way method + + Sequence weighting scheme to use on the iteration 3 and all subsequent + iterations for tree-dependent refinement. + none=all sequences have equal weight. + henikoff=Henikoff & Henikoff weighting scheme. + henikoffpb=Modified Henikoff scheme as used in PSI-BLAST. + clustalw=CLUSTALW method. + threeway=Gotoh three-way method + -weight2 prog_docs/muscle.html clustalw @@ -375,9 +450,12 @@ clustalw threeway - + + Distance1 - Distance measure for iteration 1. Defaults Kmer6_6 (for amino ) or Kmer4_6 (for nucleo) + + Distance measure for iteration 1. Defaults Kmer6_6 (for amino ) or Kmer4_6 (for nucleo) + -distance1 prog_docs/muscle.html kmer6_6 diff --git a/conf/settings/MusclePresets.xml b/conf/settings/MusclePresets.xml index 6b63ac6..04bcfb7 100644 --- a/conf/settings/MusclePresets.xml +++ b/conf/settings/MusclePresets.xml @@ -1,32 +1,42 @@ - compbio.runner.muscle.Muscle - - Protein alignment(Fastest speed) - Fastest possible speed for protein sequences. Gives acceptable quality alignments for closely related sequences - - - - - - - - - Nucleotide alignment(Fastest speed) - Fastest possible speed for nucleotide sequences. Gives acceptable quality alignments for closely related sequences - - - - - - - Large alignments (balanced) - A large number of sequences (a few thousand), or very long sequences, - then the default settings of may be too slow for practical use. - A good compromise between speed and accuracy is to run just the first two iterations of - the algorithm - - - - + compbio.runner.msa.Muscle + + + Protein alignment(Fastest speed) + + Fastest possible speed for protein sequences. Gives acceptable quality + alignments for closely related sequences + + + + + + + + + + + Nucleotide alignment(Fastest speed) + + Fastest possible speed for nucleotide sequences. Gives acceptable quality + alignments for closely related sequences + + + + + + + + + Large alignments (balanced) + + A large number of sequences (a few thousand), or very long sequences, then the default + settings of may be too slow for practical use. A good compromise between speed and + accuracy is to run just the first two iterations of the algorithm. + + + + + diff --git a/conf/settings/ProbconsLimits.xml b/conf/settings/ProbconsLimits.xml index e530fb9..974ead9 100644 --- a/conf/settings/ProbconsLimits.xml +++ b/conf/settings/ProbconsLimits.xml @@ -1,13 +1,15 @@ - compbio.runner.probcons.Probcons - - 1000 - 1000 - - - # LocalEngineExecutionLimit # - 20 - 500 - + compbio.runner.msa.Probcons + + + 1000 + 1000 + + + + # LocalEngineExecutionLimit # + 20 + 500 + diff --git a/conf/settings/ProbconsParameters.xml b/conf/settings/ProbconsParameters.xml index ddd2605..c66cdcb 100644 --- a/conf/settings/ProbconsParameters.xml +++ b/conf/settings/ProbconsParameters.xml @@ -1,6 +1,7 @@ - compbio.runner.probcons.Probcons + compbio.runner.msa.Probcons + + Output aligned - Output sequences in alignment order rather than input order + + Output sequences in alignment order rather than input order + -a prog_docs/probcons.pdf + - +--> + Rounds of pre-training before aligning the sequences - This specifies the number of rounds of EM to be applied on the set of sequences being -aligned. This option is used in case the default parameters are not appropriate for the -particular sequences being aligned; in general, this option is not recommended as it may -lead to unstable alignment parameters. + + This specifies the number of rounds of EM to be applied on the set of sequences being + aligned. This option is used in case the default parameters are not appropriate for the + particular sequences being aligned; in general, this option is not recommended as it may + lead to unstable alignment parameters. + -pre prog_docs/probcons.pdf 0 diff --git a/conf/settings/TcoffeeLimits.xml b/conf/settings/TcoffeeLimits.xml index 7e9dc9e..f45c633 100644 --- a/conf/settings/TcoffeeLimits.xml +++ b/conf/settings/TcoffeeLimits.xml @@ -1,21 +1,22 @@ - compbio.runner.tcoffee.Tcoffee - - 1000 - 1000 - - - # LocalEngineExecutionLimit # - 15 - 400 - + compbio.runner.msa.Tcoffee - - - Quick align. Very fast approximate (Speed-oriented) - 1000 - 3000 - + + 1000 + 1000 + + + # LocalEngineExecutionLimit # + 15 + 400 + + + + + Quick align. Very fast approximate (Speed-oriented) + 1000 + 3000 + diff --git a/conf/settings/TcoffeeParameters.xml b/conf/settings/TcoffeeParameters.xml index 5989d85..ba49b86 100644 --- a/conf/settings/TcoffeeParameters.xml +++ b/conf/settings/TcoffeeParameters.xml @@ -1,6 +1,6 @@ - compbio.runner.tcoffee.Tcoffee + compbio.runner.msa.Tcoffee Search sequences in PDB diff --git a/conf/settings/TcoffeePresets.xml b/conf/settings/TcoffeePresets.xml index 66e06d9..646db9c 100644 --- a/conf/settings/TcoffeePresets.xml +++ b/conf/settings/TcoffeePresets.xml @@ -1,6 +1,7 @@ - compbio.runner.tcoffee.Tcoffee + compbio.runner.msa.Tcoffee + Quick align. Very fast approximate (Speed-oriented) quickaln: Very fast, sequence type - all, accuracy - medium low @@ -8,6 +9,7 @@ + + - + -- 1.7.10.2