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diff --git a/academic/muscle5/muscle5.1 b/academic/muscle5/muscle5.1 new file mode 100644 index 0000000000..d1c2661ec2 --- /dev/null +++ b/academic/muscle5/muscle5.1 @@ -0,0 +1,93 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5. +.TH MUSCLE "1" "January 2022" "muscle 5.1" "User Commands" +.SH NAME +muscle \- Multiple alignment program of protein sequences +.SH DESCRIPTION +MUSCLE is a multiple alignment program for protein sequences. MUSCLE +stands for multiple sequence comparison by log-expectation. In the +authors tests, MUSCLE achieved the highest scores of all tested +programs on several alignment accuracy benchmarks, and is also one of +the fastest programs out there. +.SH USAGE +.SS "Align FASTA input, write aligned FASTA (AFA) output:" +.IP +muscle \fB\-align\fR input.fa \fB\-output\fR aln.afa +.PP +Align large input using Super5 algorithm if \fB\-align\fR is too expensive, +typically needed with more than a few hundred sequences: +.IP +muscle \fB\-super5\fR input.fa \fB\-output\fR aln.afa +.SS "Single replicate alignment:" +.IP +muscle \fB\-align\fR input.fa \fB\-perm\fR PERM \fB\-perturb\fR SEED \fB\-output\fR aln.afa +muscle \fB\-super5\fR input.fa \fB\-perm\fR PERM \fB\-perturb\fR SEED \fB\-output\fR aln.afa +.IP +PERM is guide tree permutation none, abc, acb, bca (default none). +SEED is perturbation seed 0, 1, 2... (default 0 = don't perturb). +.PP +Ensemble of replicate alignments, output in Ensemble FASTA (EFA) format, +EFA has one aligned FASTA for each replicate with header line "<PERM.SEED": +.IP +muscle \fB\-align\fR input.fa \fB\-stratified\fR \fB\-output\fR stratified_ensemble.efa +muscle \fB\-align\fR input.fa \fB\-diversified\fR \fB\-output\fR diversified_ensemble.afa +.HP +\fB\-replicates\fR N +.IP +Number of replicates, defaults 4, 100, 100 for stratified, +.IP +diversified, resampled. With \fB\-stratified\fR there is one +replicate per guide tree permutation, total is 4 x N. +.PP +Generate resampled ensemble from existing ensemble by sampling columns +with replacement: +.IP +muscle \fB\-resample\fR ensemble.efa \fB\-output\fR resampled.efa +.HP +\fB\-maxgapfract\fR F +.IP +Maximum fraction of gaps in a column (F=0..1, default 0.5). +.HP +\fB\-minconf\fR CC +.IP +Minimum column confidence (CC=0..1, default 0.5). +.PP +If ensemble output filename has @, then one FASTA file is generated +for each replicate where @ is replaced by perm.s, otherwise all replicates +are written to one EFA file. +.SS "Calculate disperson of an ensemble:" +.IP +muscle \fB\-disperse\fR ensemble.efa +.SS "Extract replicate with highest total CC (diversified input recommended):" +.IP +muscle \fB\-maxcc\fR ensemble.efa \fB\-output\fR maxcc.afa +.SS "Extract aligned FASTA files from EFA file:" +.IP +muscle \fB\-efa_explode\fR ensemble.efa +.SS "Convert FASTA to EFA, input has one filename per line:" +.IP +muscle \fB\-fa2efa\fR filenames.txt \fB\-output\fR ensemble.efa +.PP +Update ensemble by adding two sequences of digits to each replicate, digits +are column confidence (CC) values, e.g. "73" means CC=0.73, "++" is CC=1.0: +.IP +muscle \fB\-addconfseqs\fR ensemble.efa \fB\-output\fR ensemble_cc.efa +.PP +Calculate letter confidence (LC) values, \fB\-ref\fR specifies the alignment to +compare against the ensemble (e.g. from \fB\-maxcc\fR), output is in aligned +FASTA format with LC values 0, 1 ... 9 instead of letters: +.IP +muscle \fB\-letterconf\fR ensemble.efa \fB\-ref\fR aln.afa \fB\-output\fR letterconf.afa +.HP +\fB\-html\fR aln.html +.IP +Alignment colored by LC in HTML format. +.HP +\fB\-jalview\fR aln.features +.IP +Jalview feature file with LC values and colors. +.SS "More documentation at:" +.IP +https://drive5.com/muscle +.SH AUTHOR + This manpage was written by Andreas Tille for the Debian distribution and + can be used for any other usage of the program. |