Description

Muscle is a program for creating multiple alignments of amino acid or nucleotide sequences. This particular module uses the super5 algorithm for very big alignments. It can permutate the guide tree according to a set of flags.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

fasta{:bash}

:file

Input sequences for alignment must be in FASTA format

*.{fasta,fa,fna}

compress{:bash}

:boolean

Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded.

Output

name:type
description
pattern

alignment{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.aln{.gz,}{:bash}

:file

Multiple sequence alignment produced in gzipped FASTA format. If ‘-perm all’ is passed in ext.args, this will be multiple files per input!

*.{aln.gz}

versions_muscle{:bash}

${task.process}{:bash}

:string

The name of the process

muscle{:bash}

:string

The name of the tool

muscle -version | head -n 1 | cut -d " " -f 2 | sed "s/.linux64//"{:bash}

:eval

The expression to obtain the version of the tool

versions_pigz{:bash}

${task.process}{:bash}

:string

The name of the process

pigz{:bash}

:string

The name of the tool

pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

muscle{:bash}

:string

The name of the tool

muscle -version | head -n 1 | cut -d " " -f 2 | sed "s/.linux64//"{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

pigz{:bash}

:string

The name of the tool

pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"{:bash}

:eval

The expression to obtain the version of the tool

Tools

muscle -super5
Public Domain

Muscle v5 is a major re-write of MUSCLE based on new algorithms.

drive5.com/muscle5 drive5.com/muscle5/manual 10.1101/2021.06.20.449169

pigz

Parallel implementation of the gzip algorithm.

zlib.net/pigz zlib.net/pigz/pigz.pdf
included in
multiplesequencealign
maintainers
Github user alessiovignoli
Github user JoseEspinosa
Github user lrauschning
get in touch
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