Description

Aligns sequences using T_COFFEE

Input

Name (Type)
Description
Pattern

meta (map)

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

fasta (file)

Input sequences in FASTA format

*.{fa,fasta}

meta2 (map)

Groovy Map containing tree information
e.g. [ id:'test_tree']

tree (file)

Input guide tree in Newick format

*.{dnd}

meta3 (map)

Groovy Map containing tree information
e.g. [ id:'test_infos']

template (file)

T_coffee template file that maps sequences to the accessory information files to be used.

*

accessory_informations (file)

Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures.

*

Output

Name (Type)
Description
Pattern

meta (map)

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

alignment (file)

Alignment file.

*.{aln}

versions (file)

File containing software versions

versions.yml

Tools

tcoffee
GPL v3

A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.