modules/rapidnj

Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments.

phylogenynewickneighbour-joining

https://github.com/nf-core/modules/[...]/modules/nf-core/rapidnj

Description

Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments.

Input

name:type

description

pattern

`alignment`
`:file`

A FASTA format multiple sequence alignment file

*.{fasta,fas,fa,mfa}

Output

name:type

description

pattern

`stockholm_alignment`

`*.sth`
`:file`

An alignment in Stockholm format

*.{sth}

`phylogeny`

`*.tre`
`:file`

A phylogeny in Newick format

*.{tre}

`versions_rapidnj`

`${task.process}`
`:string`

The name of the process

`rapidnj`
`:string`

The name of the tool

`echo 2.3.2`
`:eval`

The expression to obtain the version of the tool

`versions_biopython`

`${task.process}`
`:string`

The name of the process

`biopython`
`:string`

The name of the tool

`python -c "import Bio; print(Bio.version)"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`rapidnj`
`:string`

The name of the tool

`echo 2.3.2`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`biopython`
`:string`

The name of the tool

`python -c "import Bio; print(Bio.version)"`
`:eval`

The expression to obtain the version of the tool

Tools

rapidnj
GPL v2

RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations.

birc.au.dk/software/rapidnj https://github.com/somme89/rapidNJ 10.1007/978-3-540-87361-7_10

modules/rapidnj

Description

Input

`alignment`
`:file`

Output

`stockholm_alignment`

`*.sth`
`:file`

`phylogeny`

`*.tre`
`:file`

`versions_rapidnj`

`${task.process}`
`:string`

`rapidnj`
`:string`

`echo 2.3.2`
`:eval`

`versions_biopython`

`${task.process}`
`:string`

`biopython`
`:string`

`python -c "import Bio; print(Bio.version)"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`rapidnj`
`:string`

`echo 2.3.2`
`:eval`

`${task.process}`
`:string`

`biopython`
`:string`

`python -c "import Bio; print(Bio.version)"`
`:eval`

Tools

rapidnj
GPL v2

maintainers

get in touch

modules/rapidnj

Description

Input

alignment:file

Output

stockholm_alignment

*.sth:file

phylogeny

*.tre:file

versions_rapidnj

${task.process}:string

rapidnj:string

echo 2.3.2:eval

versions_biopython

${task.process}:string

biopython:string

python -c "import Bio; print(Bio.__version__)":eval

Topics

versions

${task.process}:string

rapidnj:string

echo 2.3.2:eval

${task.process}:string

biopython:string

python -c "import Bio; print(Bio.__version__)":eval

Tools

rapidnj GPL v2

maintainers

get in touch

`alignment`
`:file`

`stockholm_alignment`

`*.sth`
`:file`

`phylogeny`

`*.tre`
`:file`

`versions_rapidnj`

`${task.process}`
`:string`

`rapidnj`
`:string`

`echo 2.3.2`
`:eval`

`versions_biopython`

`${task.process}`
`:string`

`biopython`
`:string`

`python -c "import Bio; print(Bio.version)"`
`:eval`

`versions`

`${task.process}`
`:string`

`rapidnj`
`:string`

`echo 2.3.2`
`:eval`

`${task.process}`
`:string`

`biopython`
`:string`

`python -c "import Bio; print(Bio.version)"`
`:eval`

rapidnj
GPL v2