Description

splits an alignment into reference and query parts

Input

Name (Type)
Description
Pattern

meta (map)

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

]

refaln (file)

reference alignment in any supported format including phylip and fasta, may be gzipped

*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}

fullaln (file)

full alignment in any supported format to split into reference and query alignments

*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

query (file)

query sequence alignment in gzipped fasta format

reference (file)

reference sequence alignment in gzipped fasta format

versions (file)

File containing software versions

versions.yml
included in
ampliseq phyloplace
maintainer
Github user erikrikarddaniel
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

epang
GNU Affero General Public License v3.0

Massively parallel phylogenetic placement of genetic sequences

github.com/Pbdas/epa-ng github.com/Pbdas/epa-ng/wiki/Full-Stack-Example https://github.com/Pbdas/epa-ng 10.1093/sysbio/syy054