Description

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

Input

Name
Description
Pattern

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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
Description
Pattern

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Tools

iqtree Documentation

Efficient phylogenomic software by maximum likelihood.

https://github.com/iqtree/iqtree2doi: 10.1093/molbev/msaa015License: GPL v2-or-later
Authors