Description

hmmalign from the HMMER suite aligns a number of sequences to an HMM profile

Input

name:type
description
pattern

meta

:map

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

fasta

:file

Amino acid or nucleotide gzipped compressed fasta file

*.{fna.gz,faa.gz,fasta.gz,fa.gz}

hmm

:file

A gzipped HMM file

*.hmm.gz

Output

name:type
description
pattern

sto

meta

:map

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

*.sto.gz

:file

Multiple alignment in gzipped Stockholm format

*.sto.gz

versions_hmmer

${task.process}

:string

The name of the process

hmmer

:string

The name of the tool

hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

hmmer

:string

The name of the tool

hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'

:eval

The expression to obtain the version of the tool

Tools

hmmer
BSD-3-Clause

Biosequence analysis using profile hidden Markov models

http://hmmer.org http://hmmer.org/documentation 10.1371/journal.pcbi.1002195
included in
ampliseqphyloplaceproteinfamilies
maintainers
Github user erikrikarddaniel
Github user jfy133
Github user vagkaratzas
get in touch
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