modules/iqtree

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

phylogenynewickmaximum likelihood

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

Description

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

Input

name:type

description

pattern

`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

name:type

description

pattern

`phylogeny`

`meta:file`

A phylogeny in Newick format

*.{treefile}

`*.treefile:file`

A phylogeny in Newick format

*.{treefile}

`report`

`meta:file`

Main report file containing computational results as well as a textual visualization of the final tree

*.{iqtree}

`*.iqtree:file`

Main report file containing computational results as well as a textual visualization of the final tree

*.{iqtree}

`mldist`

`meta:file`

File containing the pairwise maximum likelihood distances as a matrix

*.{mldist}

`*.mldist:file`

File containing the pairwise maximum likelihood distances as a matrix

*.{mldist}

`lmap_svg`

`meta:file`

File containing likelihood mapping analysis results in .svg format (-lmap/-lmclust)

*.lmap.svg

`*.lmap.svg:file`

File containing likelihood mapping analysis results in .svg format (-lmap/-lmclust)

*.lmap.svg

`lmap_eps`

`meta:file`

File containing likelihood mapping analysis results in .eps format (-lmap/-lmclust)

*.lmap.eps

`*.lmap.eps:file`

File containing likelihood mapping analysis results in .eps format (-lmap/-lmclust)

*.lmap.eps

`lmap_quartetlh`

`meta:file`

File containing quartet log-likelihoods (-wql)

*.lmap.quartetlh

`*.lmap.quartetlh:file`

File containing quartet log-likelihoods (-wql)

*.lmap.quartetlh

`sitefreq_out`

`meta:file`

File containing site frequency profiles (-ft)

*.sitefreq

`*.sitefreq:file`

File containing site frequency profiles (-ft)

*.sitefreq

`bootstrap`

`meta:file`

File containing all bootstrap trees (-wbt/-wbtl)

*.ufboot

`*.ufboot:file`

File containing all bootstrap trees (-wbt/-wbtl)

*.ufboot

`state`

`meta:file`

File containing ancestral sequences for all nodes of the tree by empirical Bayesian method (-asr)

*.{state}

`*.state:file`

File containing ancestral sequences for all nodes of the tree by empirical Bayesian method (-asr)

*.{state}

`contree`

`meta:file`

File containing consensus tree (-con/-bb)

*.{contree}

`*.contree:file`

File containing consensus tree (-con/-bb)

*.{contree}

`nex`

`meta:file`

File containing consensus network (-net/-bb)

*.{nex}

`*.nex:file`

File containing consensus network (-net/-bb)

*.{nex}

`splits`

`meta:file`

File containing consensus network in star-dot format (-wsplits)

*.{splits}

`*.splits:file`

File containing consensus network in star-dot format (-wsplits)

*.{splits}

`suptree`

`meta:file`

File containing tree with assigned support values based on supplied “target” tree (-sup)

*.{suptree}

`*.suptree:file`

File containing tree with assigned support values based on supplied “target” tree (-sup)

*.{suptree}

`alninfo`

`meta:file`

File containing alignment site statistics (-alninfo)

*.{alninfo}

`*.alninfo:file`

File containing alignment site statistics (-alninfo)

*.{alninfo}

`partlh`

`meta:file`

File containing partition log-likelihoods (-wpl)

*.{partlh}

`*.partlh:file`

File containing partition log-likelihoods (-wpl)

*.{partlh}

`siteprob`

`meta:file`

File containing site posterior probabilities (-wspr/-wspm/-wspmr)

*.{siteprob}

`*.siteprob:file`

File containing site posterior probabilities (-wspr/-wspm/-wspmr)

*.{siteprob}

`sitelh`

`meta:file`

File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr)

*.{sitelh}

`*.sitelh:file`

File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr)

*.{sitelh}

`treels`

`meta:file`

File containing all locally optimal trees (-wt)

*.{treels}

`*.treels:file`

File containing all locally optimal trees (-wt)

*.{treels}

`rate`

`meta:file`

File containing inferred site-specific evolutionary rates (-wsr)

*.{rate}

`*.rate :file`

File containing inferred site-specific evolutionary rates (-wsr)

*.{rate}

`mlrate`

`meta:file`

File containing site-specific substitution rates determined by maximum likelihood (—mlrate)

*.{mlrate}

`*.mlrate:file`

File containing site-specific substitution rates determined by maximum likelihood (—mlrate)

*.{mlrate}

`exch_matrix`

`meta:file`

File containing the exchangeability matrix obtained from the optimization (—link-exchange-rates)

GTRPMIX.nex

`GTRPMIX.nex:file`

File containing the exchangeability matrix obtained from the optimization (—link-exchange-rates)

GTRPMIX.nex

`log`

`meta:file`

Log file of entire run

*.{log}

`*.log:file`

Log file of entire run

*.{log}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

iqtree
GPL v2-or-later

Efficient phylogenomic software by maximum likelihood.

http://www.iqtree.org http://www.iqtree.org/doc https://github.com/iqtree/iqtree2 10.1093/molbev/msaa015