X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=dundee-conf%2Fsettings%2FMuscleParameters.xml;fp=dundee-conf%2Fsettings%2FMuscleParameters.xml;h=11c36d8f0a62cb53a5d55bfac4920ce9a0287e7a;hb=50bb3e70f53817b1174b79003f4826c95b25ff6e;hp=0000000000000000000000000000000000000000;hpb=cfbceac612220d0a877942f7fb6658a5848d1ccf;p=jabaws.git diff --git a/dundee-conf/settings/MuscleParameters.xml b/dundee-conf/settings/MuscleParameters.xml new file mode 100644 index 0000000..11c36d8 --- /dev/null +++ b/dundee-conf/settings/MuscleParameters.xml @@ -0,0 +1,289 @@ + + + compbio.runner.muscle.Muscle + + Group sequences + Group sequences by similarity (this is the default) or preserve the input order + -group + -stable + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + -stable + + + Anchor optimisation + Enable/disable anchor optimization in tree dependent refinement iterations + -anchors + -noanchors + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + -anchors + + + Root alignment computation method + Use Steven Brenner's method for computing the root alignment. + -brenner + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + + + + dimer + Use dimer approximation for the SP score (faster, slightly less accurate) + -dimer + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + + + Diagonal + Use diagonal optimizations. Faster, especially for closely related sequences, but may be less accurate. + -diags + + + Diagonal 1 + Use diagonal optimizations in first iteration (faster for similar sequences) + -diags1 + + + 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 + -sp + -sv + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + -le + + + + Sequence type + Sequence type - Amino acid/Nucleotide + -seqtype + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + auto + auto + protein + nucleo + + + Maxiters + Maximum number of iterations (integer, default 16) + -maxiters + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + 16 + + Integer + 1 + 100 + + + + Matrix + Substitution Matrix to use + -matrix + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.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 + + + Gap open penalty + Gap opening penalty. Must be negative + -gapopen + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + -12.0 + + Float + -100 + 0 + + + + Gap extension penalty + Gap extension penalty. Must be negative + -gapextend + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + -1.0 + + Float + -100 + 0 + + + + Center + Center parameter. Should be negative. + -center + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + 0.0 + + Float + -100 + 0 + + + + Hydro + Window size for determining whether a region is hydrophobic. + -hydro + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + 5 + + Integer + 0 + 100 + + + + Hydrofactor + Multiplier for gap open/close penalties in hydrophobic regions. + -hydrofactor + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + 1.2 + + Float + 0 + 10 + + + + cluster1 + Clustering method to use on the iteration 1 + -cluster1 + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + upgma + upgma + + + cluster2 + Clustering method to use on the iteration 2 and all subsequent itarations + -cluster2 + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.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 + -weight1 + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + clustalw + none + henikoff + henikoffpb + gsc + 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 + -weight2 + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + clustalw + none + henikoff + henikoffpb + gsc + clustalw + threeway + + + Distance1 + Distance measure for iteration 1. Defaults Kmer6_6 (for amino ) or Kmer4_6 (for nucleo) + -distance1 + http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html + kmer6_6 + kmer6_6 + kmer20_3 + kbit20_3 + kmer20_4 + kmer4_6 + +