Nextflow Registry | nf-core/iqtree@0.0.0-6c4ed3a

nf-core/iqtree @ 0.0.0-6c4ed3a

Produces a Newick format phylogeny from a multiple sequence alignment using the maximum likelihood algorithm. Capable of bacterial genome size alignments.

phylogeny newick maximum likelihood

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @avantonder @aunderwo

Maintainers: @avantonder @aunderwo

Summary

Produces a Newick format phylogeny from a multiple sequence alignment using the maximum likelihood algorithm. Capable of bacterial genome size alignments.

Get started

Add the following snippet to your workflow script to include this module.

include { IQTREE } from 'nf-core/iqtree'

License

MIT License

Process

`Name`	`IQTREE`

Input 13 channels

#1 tuple

`meta` map	Groovy map containing sample information for the alignment/tree file, e.g. [ id: 'test' ]
`alignment` file	One or more input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format or a directory of such files (-s) `*.{fasta,fas,fa,mfa,phy,aln,nex,nexus,msf}`
`tree` file	File containing one or multiple phylogenetic trees (-t): - Single tree used e.g. as starting tree for tree search - Set of trees used e.g. for distance computation, consensus tree construction `*.{tre,tree,treefile,newick,nwk,nex,nexus}`

`tree_te` file	File containing single phylogenetic tree (-te) Use cases: - fixed user tree to skip tree search - ancestral sequence reconstruction `*.{tre,tree,treefile,newick,nwk,nex,nexus}`

`lmclust` file	NEXUS file containing taxon clusters for quartet mapping analysis (-lmclust) `*.nex{us}`

`mdef` file	NEXUS model file defining new models (-mdef) `*.nex{us}`

`partitions_equal` file	Partition file for edge-equal partition model, all partitions share same set of branch lengths (-q) `*.{nex,nexus,tre,tree,treefile}`

`partitions_proportional` file	Partition file for edge-equal partition model, all partitions share same set of branch lengths (-spp) `*.{nex,nexus,tre,tree,treefile}`

`partitions_unlinked` file	Partition file for edge-equal partition model, all partitions share same set of branch lengths (-sp) `*.{nex,nexus,tre,tree,treefile}`

`guide_tree` file	File containing guide tree for inference of site frequency profiles (-ft) `*.{nex,nexus,tre,tree,treefile}`

`sitefreq_in` file	Site frequency file (-fs) `*.sitefreq`

`constraint_tree` file	File containing opological constraint tree in NEWICK format. The constraint tree can be a multifurcating tree and need not to include all taxa. (-g) `*.{nwk,newick}`

`trees_z` file	File containing a set of trees for which log-likelihoods should be computed (-z)

`suptree` file	File containing input “target” tree, support values are extracted from trees passed via -t, and mapped onto the target tree (-sup)

`trees_rf` file	File containing a second tree set (-rf). Used for computing the distance to the primary tree set (`tree`) `*.{tre,tree,treefile,newick,nwk,nex,nexus}`

Output 23 channels

#1 log tuple

`meta` map	Groovy Map containing sample information
`*.log` file	Log file of entire run `*.{log}`

#2 nex tuple

`meta` map	Groovy Map containing sample information
`*.nex` file	File containing consensus network (-net/-bb) `*.{nex}`

#3 rate tuple

`meta` map	Groovy Map containing sample information
`*.rate` file	File containing inferred site-specific evolutionary rates (-wsr) `*.{rate}`

#4 state tuple

`meta` map	Groovy Map containing sample information
`*.state` file	File containing ancestral sequences for all nodes of the tree by empirical Bayesian method (-asr) `*.{state}`

#5 mldist tuple


`meta` map	Groovy Map containing sample information