Description

Efficient phylogenetic tree reconstruction for sequences using the CMAPLE algorithm

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 FASTA, PHYLIP, or MAPLE format. Can be gzipped on uncompressed.

*.{fa,fasta,faa,fna,fas,aln,afa,phy,phylip,maple}{.gz,}

newick{:bash}

:file

A Newick formatted tree based on multiple sequence alignment

*.{newick,nwk,treefile}

Output

name:type
description
pattern

treefile{:bash}

meta{:bash}

:map

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

*.treefile{:bash}

:file

Maximum likelihood phylogenetic tree in Newick format

*.treefile

log{:bash}

meta{:bash}

:map

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

*.log{:bash}

:file

Log file containing detailed information about the tree reconstruction process

*.log

versions_cmaple{:bash}

${task.process}{:bash}

:string

The name of the process

cmaple{:bash}

:string

The name of the tool

cmaple --help | grep -m1 -oE "[0-9]+(\.[0-9]+)+"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

cmaple{:bash}

:string

The name of the tool

cmaple --help | grep -m1 -oE "[0-9]+(\.[0-9]+)+"{:bash}

:eval

The expression to obtain the version of the tool

Tools

cmaple
GPL-2.0

CMAPLE (Comprehensive Maximum-likelihood Analysis for Phylogenetic Likelihood Estimation) is an efficient implementation of the MAPLE algorithm for phylogenetic tree reconstruction, particularly optimized for pathogen sequences with low divergence such as SARS-CoV-2. It is integrated within IQ-TREE.

github.com/iqtree/cmaple github.com/iqtree/cmaple/wiki/User-Manual https://github.com/iqtree/cmaple 10.1093/molbev/msae134
included in
proteinfamilies
maintainer
Github user vagkaratzas
get in touch
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