X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=testsrc%2Ftestdata%2FMuscleParameters.xml;fp=testsrc%2Ftestdata%2FMuscleParameters.xml;h=c27d86a7816ee24af69a090f63030b03dbf7fa97;hb=babb6decd107f2769f1fbcce00afcda16bd07110;hp=0000000000000000000000000000000000000000;hpb=8bb35115758f447219bef40d3e7c1f1ac9ba3ed6;p=proteocache.git diff --git a/testsrc/testdata/MuscleParameters.xml b/testsrc/testdata/MuscleParameters.xml new file mode 100644 index 0000000..c27d86a --- /dev/null +++ b/testsrc/testdata/MuscleParameters.xml @@ -0,0 +1,389 @@ + + + compbio.runner.muscle.Muscle + + Group sequences + Group sequences by similarity (this is the default) or preserve the input order + -group + prog_docs/muscle.html + -group + + + + Anchor optimisation + 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. + -brenner + prog_docs/muscle.html + + + + dimer + 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. + -diags + prog_docs/muscle.html + + + Diagonal 1 + 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 + -sp + -sv + prog_docs/muscle.html + -le + + + + Sequence type + Sequence type - Amino acid/Nucleotide + -seqtype + prog_docs/muscle.html + auto + auto + protein + dna + rna + + + Maxiters + Maximum number of iterations (integer, default 16) + -maxiters + prog_docs/muscle.html + 16 + + Integer + 1 + 100 + + + + + Diagonal break + Maximum distance between two diagonals that allows them to merge into one diagonal + -diagbreak + prog_docs/muscle.html + 1 + + Integer + 1 + 100 + + + + Diagonal length + Minimum length of diagonal + -diaglength + prog_docs/muscle.html + 24 + + Integer + 2 + 100 + + + + Diagonal margin + Discard this many positions at ends of diagonal + -diagmargin + prog_docs/muscle.html + 5 + + Integer + 1 + 100 + + + + Anchor spacing + Minimum spacing between anchor columns + -anchorspacing + prog_docs/muscle.html + 32 + + Integer + 2 + 1000 + + + + + Gap open penalty + Gap opening penalty. Must be negative + -gapopen + prog_docs/muscle.html + -12.0 + + Float + -100 + 0 + + + + Gap extension penalty + Gap extension penalty. Must be negative + -gapextend + prog_docs/muscle.html + -1.0 + + Float + -100 + 0 + + + + Center + Center parameter. Should be negative. + -center + prog_docs/muscle.html + 0.0 + + Float + -100 + 0 + + + + Hydro + Window size for determining whether a region is hydrophobic. + -hydro + prog_docs/muscle.html + 5 + + Integer + 0 + 100 + + + + Hydrofactor + Multiplier for gap open/close penalties in hydrophobic regions. + -hydrofactor + prog_docs/muscle.html + 1.2 + + Float + 0 + 10 + + + + Minimum anchor score + 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 + 0 + 10 + + + + Minimum smoothed anchor score + 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 + 0 + 10 + + + + cluster1 + 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 + -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 + -weight1 + prog_docs/muscle.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 + prog_docs/muscle.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 + prog_docs/muscle.html + kmer6_6 + kmer6_6 + kmer20_3 + kbit20_3 + kmer20_4 + kmer4_6 + +