modules/muscle

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two

msamultiple sequence alignmentphylogeny

https://github.com/nf-core/modules/[...]/modules/nf-core/muscle

Description

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`fasta:file`

Input sequences for alignment must be in FASTA format

*.{fasta,fa,fna}

Output

name:type

description

pattern

`aligned_fasta`

`meta:file`

Multiple sequence alignment produced in FASTA format

*.{afa}

`*.afa:file`

Multiple sequence alignment produced in FASTA format

*.{afa}

`phyi`

`meta:file`

Multiple sequence alignment produced in PHYLIP interleaved format

*.{phyi}

`*.phyi:file`

Multiple sequence alignment produced in PHYLIP interleaved format

*.{phyi}

`phys`

`meta:file`

Multiple sequence alignment produced in PHYLIP sequential format

*.{phys}

`*.phys:file`

Multiple sequence alignment produced in PHYLIP sequential format

*.{phys}

`clustalw`

`meta:file`

Multiple sequence alignment produced in ClustalW format without base/residue numbering

*.{clw}

`*.clw:file`

Multiple sequence alignment produced in ClustalW format without base/residue numbering

*.{clw}

`html`

`meta:file`

Multiple sequence alignment produced in HTML format

*.{html}

`*.html:file`

Multiple sequence alignment produced in HTML format

*.{html}

`msf`

`meta:file`

GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW)

*.{msf}

`*.msf:file`

GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW)

*.{msf}

`tree`

`meta:file`

NJ or UPGMA tree in Newick format produced from a multiple sequence alignment

*.{tree}

`*.tree:file`

NJ or UPGMA tree in Newick format produced from a multiple sequence alignment

*.{tree}

`log`

`*.log:file`

Log file of MUSCLE run

*{.log}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

muscle
http://www.drive5.com/muscle/manual/license.html

MUSCLE is a multiple sequence alignment tool with high accuracy and throughput

drive5.com/muscle http://www.drive5.com/muscle/muscle.html#_Toc81224840 10.1093/nar/gkh340

modules/muscle

Description

Input

meta:map

fasta:file

Output

aligned_fasta

meta:file

*.afa:file

phyi

meta:file

*.phyi:file

phys

meta:file

*.phys:file

clustalw

meta:file

*.clw:file

html

meta:file

*.html:file

msf

meta:file

*.msf:file

tree

meta:file

*.tree:file

log

*.log:file

versions

versions.yml:file

Tools

muscle http://www.drive5.com/muscle/manual/license.html

`meta:map`

`fasta:file`

`aligned_fasta`

`meta:file`

`*.afa:file`

`phyi`

`meta:file`

`*.phyi:file`

`phys`

`meta:file`

`*.phys:file`

`clustalw`

`meta:file`

`*.clw:file`

`html`

`meta:file`

`*.html:file`

`msf`

`meta:file`

`*.msf:file`

`tree`

`meta:file`

`*.tree:file`

`log`

`*.log:file`

`versions`

`versions.yml:file`

muscle
http://www.drive5.com/muscle/manual/license.html