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