academic/muscle5: Added (MUSCLE 5: Next-generation MUSCLE)

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 93 insertions, 0 deletions

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+.\" 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.