Description

Multiple Sequence Alignment using Graph Clustering

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing the fasta meta information
e.g. [ id:'test', single_end:false ]

meta2 (map)

Groovy Map containing sample information for the specified guide tree (if supplied)
e.g. [ id:'test', single_end:false ]

fasta (file)

Input sequences in FASTA format.

*.{fa,fna,fasta}

tree (file)

Optional path to a file containing a guide tree in newick format to use as input. If empty, or overwritten by passing -t [fasttree|fasttree-noml|clustal|parttree], MAGUS will construct its own guide tree. If empty, fasttree is used as a default.

*.{dnd,tree}

compress (boolean)

Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded.

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

alignment (file)

File containing the output alignment, in FASTA format containing gaps. The sequences may be in a different order than in the input FASTA. The output file may or may not be gzipped, depending on the value supplied to compress.

*.aln{.gz,}
included in
multiplesequencealign
maintainer
Github user lrauschning
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Tools

magus
MIT

Multiple Sequence Alignment using Graph Clustering

github.com/vlasmirnov/MAGUS 10.1093/bioinformatics/btaa992