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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

sthlm (file)

Multiple alignment in gzipped Stockholm format

*.sthlm.gz
included in
ampliseq phyloplace
authors
Github user erikrikarddaniel Github user jfy133
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

hmmer
BSD-3-Clause

Biosequence analysis using profile hidden Markov models

http://hmmer.org http://hmmer.org/documentation.html 10.1371/journal.pcbi.1002195