X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2Fsettings%2FMuscleParameters.xml;h=135ca2a4933a3e04c5bc1434921391836167dce5;hb=4a317845b7f26b5e93bd4d9f5ec350083d3e35b0;hp=08ff4524e51a9d3d20f0252715d9c95dfbfba1ef;hpb=2df9339bdc230e2db3c36ed85960bcd13a225188;p=jabaws.git 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