Description

ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes those that display characteristics poor phylogenetic signal.

Input

name:type
description
pattern

meta{:bash}

:map

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

aln{:bash}

:file

Multiple sequence alignment file in various supported formats.

*.{fa,fasta,fa,fna,faa,alnfaa,aln,sto,stk,mauve,alignment,clustal}

out_format{:bash}

:string

Output format (aln,msa,fas,etc.), default is clipkit.

*

Output

name:type
description
pattern

clipkit{:bash}

meta{:bash}

:map

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

${prefix}.${out_extension}{:bash}

:file

Trimmed multiple sequence alignment file

*.*

log{:bash}

meta{:bash}

:map

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

${prefix}.log{:bash}

:file

Log file with statistics from the tool’s execution

*.log

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
proteinfamilies
maintainer
Github user vagkaratzas
get in touch
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