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{:bash}

:map

Groovy map containing sample information for the alignment/tree file, e.g. [ id: ‘test’ ]

alignment{:bash}

: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{:bash}

: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{:bash}

: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{:bash}

:file

NEXUS file containing taxon clusters for quartet mapping analysis (-lmclust)

*.nex{us}

mdef{:bash}

:file

NEXUS model file defining new models (-mdef)

*.nex{us}

partitions_equal{:bash}

:file

Partition file for edge-equal partition model, all partitions share same set of branch lengths (-q)

*.{nex,nexus,tre,tree,treefile}

partitions_proportional{:bash}

:file

Partition file for edge-equal partition model, all partitions share same set of branch lengths (-spp)

*.{nex,nexus,tre,tree,treefile}

partitions_unlinked{:bash}

:file

Partition file for edge-equal partition model, all partitions share same set of branch lengths (-sp)

*.{nex,nexus,tre,tree,treefile}

guide_tree{:bash}

:file

File containing guide tree for inference of site frequency profiles (-ft)

*.{nex,nexus,tre,tree,treefile}

sitefreq_in{:bash}

:file

Site frequency file (-fs)

*.sitefreq

constraint_tree{:bash}

: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{:bash}

:file

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

suptree{:bash}

:file

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

trees_rf{:bash}

: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{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.treefile{:bash}

:file

A phylogeny in Newick format

*.{treefile}

report{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.iqtree{:bash}

:file

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

*.{iqtree}

mldist{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.mldist{:bash}

:file

File containing the pairwise maximum likelihood distances as a matrix

*.{mldist}

lmap_svg{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.lmap.svg{:bash}

:file

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

*.lmap.svg

lmap_eps{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.lmap.eps{:bash}

:file

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

*.lmap.eps

lmap_quartetlh{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.lmap.quartetlh{:bash}

:file

File containing quartet log-likelihoods (-wql)

*.lmap.quartetlh

sitefreq_out{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.sitefreq{:bash}

:file

File containing site frequency profiles (-ft)

*.sitefreq

bootstrap{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.ufboot{:bash}

:file

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

*.ufboot

state{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.state{:bash}

:file

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

*.{state}

contree{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.contree{:bash}

:file

File containing consensus tree (-con/-bb)

*.{contree}

nex{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.nex{:bash}

:file

File containing consensus network (-net/-bb)

*.{nex}

splits{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.splits{:bash}

:file

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

*.{splits}

suptree{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.suptree{:bash}

:file

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

*.{suptree}

alninfo{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.alninfo{:bash}

:file

File containing alignment site statistics (-alninfo)

*.{alninfo}

partlh{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.partlh{:bash}

:file

File containing partition log-likelihoods (-wpl)

*.{partlh}

siteprob{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.siteprob{:bash}

:file

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

*.{siteprob}

sitelh{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.sitelh{:bash}

:file

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

*.{sitelh}

treels{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.treels{:bash}

:file

File containing all locally optimal trees (-wt)

*.{treels}

rate{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.rate {:bash}

:file

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

*.{rate}

mlrate{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.mlrate{:bash}

:file

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

*.{mlrate}

exch_matrix{:bash}

meta{:bash}

:map

Groovy Map containing sample information

GTRPMIX.nex{:bash}

:file

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

GTRPMIX.nex

log{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.log{:bash}

:file

Log file of entire run

*.{log}

versions{:bash}

versions.yml{:bash}

: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
included in
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