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academic/muscle5: Added (MUSCLE 5: Next-generation MUSCLE)
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
d5622d171b
commit
1f43c07f3c
6 changed files with 273 additions and 0 deletions
28
academic/muscle5/README
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28
academic/muscle5/README
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MUSCLE 5: Next-generation MUSCLE
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Muscle v5 is a major re-write of MUSCLE based on new algorithms.
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* Highest accuracy, scalable to thousands of sequences:
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Compared to previous versions, Muscle v5 is much more accurate, is often
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faster, and scales to much larger datasets. At the time of writing (late
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2021), Muscle v5 has the highest scores on multiple alignment benchmarks
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including Balibase, Bralibase, Prefab and Balifam. It can align tens of
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thousands of sequences with high accuracy on a low-cost commodity
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computer (say, an 8-core Intel CPU with 32 Gb RAM). On large datasets,
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Muscle v5 is 20-30% more accurate than MAFFT and Clustal-Omega.
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* Alignment ensembles:
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Muscle v5 can generate ensembles of high-accuracy alternative
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alignments. All replicates have equal average accuracy on benchmark
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test, including the MSA made with default parameters. By comparing
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results of downstream analysis (trees, structure prediction...) on
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different replicates, you can assess the effects of alignment errors on
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your study.
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* Manual:
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https://drive5.com/muscle5/manual/
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* Reference (included in the package)
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R.C. Edgar (2021) "MUSCLE v5 enables improved estimates of phylogenetic
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tree confidence by ensemble bootstrapping"
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https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full.pdf
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5
academic/muscle5/References
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5
academic/muscle5/References
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References
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R.C. Edgar (2021) "MUSCLE v5 enables improved estimates of phylogenetic
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tree confidence by ensemble bootstrapping"
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https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full.pdf
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93
academic/muscle5/muscle5.1
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93
academic/muscle5/muscle5.1
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.\" 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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118
academic/muscle5/muscle5.SlackBuild
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118
academic/muscle5/muscle5.SlackBuild
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#!/bin/bash
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# Slackware build script for muscle5
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# Copyright 2022 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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cd $(dirname $0) ; CWD=$(pwd)
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PRGNAM=muscle5
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VERSION=${VERSION:-5.1}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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SRCNAM=muscle
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
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# the name of the created package would be, and then exit. This information
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# could be useful to other scripts.
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if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
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echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
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exit 0
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fi
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $SRCNAM-$VERSION
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tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
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cd $SRCNAM-$VERSION
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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cd src
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# do not create static executable
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sed -i "s:LDFLAGS += -static:#LDFLAGS += -static:" Makefile
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make CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS"
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install -D -m755 Linux/$SRCNAM $PKG/usr/bin/$PRGNAM
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cd ..
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# Thanks to Debian for the man page
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mkdir -p $PKG/usr/man/man1
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cp $CWD/$PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1
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# The Makefile strips the binary...
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#find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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# | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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find $PKG/usr/man -type f -exec gzip -9 {} \;
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for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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CONTRIBUTING.md LICENSE README.md \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
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10
academic/muscle5/muscle5.info
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10
academic/muscle5/muscle5.info
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PRGNAM="muscle5"
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VERSION="5.1"
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HOMEPAGE="https://github.com/rcedgar/muscle"
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DOWNLOAD="https://github.com/rcedgar/muscle/archive/v5.1/muscle-5.1.tar.gz"
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MD5SUM="99b5ef38a119994e7a8f0ea7a12b5987"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES=""
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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19
academic/muscle5/slack-desc
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19
academic/muscle5/slack-desc
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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muscle5: muscle5 (MUSCLE 5: Next-generation MUSCLE)
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muscle5:
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muscle5: Muscle v5 is a major re-write of MUSCLE based on new algorithms.
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muscle5: Compared to previous versions, Muscle v5 is much more accurate,
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muscle5: faster, and scales to much larger datasets.
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muscle5:
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muscle5: https://drive5.com/muscle5/
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muscle5: https://drive5.com/muscle5/manual/
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muscle5:
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muscle5:
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muscle5:
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