modules/iqtree

Produces a Newick format phylogeny from a multiple sequence alignment using the maxium 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 maxium 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)

Input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format (-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` (file)

A phylogeny in Newick format

*.{treefile}

`report` (file)

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

*.{iqtree}

`mldist` (file)

File containing the pairwise maximum
likelihood distances as a matrix

*.{mldist}

`lmap_svg` (file)

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

*.lmap.svg

`lmap_eps` (file)

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

*.lmap.eps

`lmap_quartetlh` (file)

File containing quartet log-likelihoods (-wql)

*.lmap.quartetlh

`sitefreq_out` (file)

File containing site frequency profiles (-ft)

*.sitefreq

`bootstrap` (file)

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

*.ufboot

`state` (file)

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

*.{state}

`contree` (file)

File containing consensus tree (-con/-bb)

*.{contree}

`nex` (file)

File containing consensus network (-net/-bb)

*.{nex}

`splits` (file)

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

*.{splits}

`suptree` (file)

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

*.{suptree}

`alninfo` (file)

File containing alignment site statistics (-alninfo)

*.{alninfo}

`partlh` (file)

File containing partition log-likelihoods (-wpl)

*.{partlh}

`siteprob` (file)

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

*.{siteprob}

`sitelh` (file)

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

*.{sitelh}

`treels` (file)

File containing all locally optimal trees (-wt)

*.{treels}

`rate` (file)

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

*.{rate}

`mlrate` (file)

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

*.{mlrate}

`exch_matrix` (file)

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

GTRPMIX.nex

`log` (file)

Log file of entire run

*.{log}

`versions` (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

modules/iqtree

Description

Input

meta (map)

alignment (file)

tree (file)

tree_te (file)

lmclust (file)

mdef (file)

partitions_equal (file)

partitions_proportional (file)

partitions_unlinked (file)

guide_tree (file)

sitefreq_in (file)

constraint_tree (file)

trees_z (file)

suptree (file)

trees_rf (file)

Output

phylogeny (file)

report (file)

mldist (file)

lmap_svg (file)

lmap_eps (file)

lmap_quartetlh (file)

sitefreq_out (file)

bootstrap (file)

state (file)

contree (file)

nex (file)

splits (file)

suptree (file)

alninfo (file)

partlh (file)

siteprob (file)

sitelh (file)

treels (file)

rate (file)

mlrate (file)

exch_matrix (file)

log (file)

versions (file)

included in

maintainers

get in touch

Tools

iqtree GPL v2-or-later

`meta` (map)

`alignment` (file)

`tree` (file)

`tree_te` (file)

`lmclust` (file)

`mdef` (file)

`partitions_equal` (file)

`partitions_proportional` (file)

`partitions_unlinked` (file)

`guide_tree` (file)

`sitefreq_in` (file)

`constraint_tree` (file)

`trees_z` (file)

`suptree` (file)

`trees_rf` (file)

`phylogeny` (file)

`report` (file)

`mldist` (file)

`lmap_svg` (file)

`lmap_eps` (file)

`lmap_quartetlh` (file)

`sitefreq_out` (file)

`bootstrap` (file)

`state` (file)

`contree` (file)

`nex` (file)

`splits` (file)

`suptree` (file)

`alninfo` (file)

`partlh` (file)

`siteprob` (file)

`sitelh` (file)

`treels` (file)

`rate` (file)

`mlrate` (file)

`exch_matrix` (file)

`log` (file)

`versions` (file)

iqtree
GPL v2-or-later