iqtree

Tags: phylogeny tree maximum-likelihood bootstrap model-selection iqtree run-scope

Efficient phylogenomic inference using Maximum Likelihood.

Uses IQ-TREE to construct a maximum-likelihood phylogenetic tree from a multiple sequence alignment. It automatically determines the best-fit substitution model (via ModelFinder) and assesses branch support using the Ultrafast Bootstrap approximation.

Inputs

record (
    meta: Record,
    aln: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
aln	Path	Multiple sequence alignment in FASTA, PHYLIP, or NEXUS format

Outputs

record (
    meta: Record,
    aln: Path,
    nwk: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
aln	Path	The input alignment (passed through)
nwk	Path	The final maximum-likelihood phylogenetic tree (Newick format)
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

IQ-TREE Parameters

Parameter	Type	Default	Description
--iqtree_model	string	HKY	Substitution model name
--iqtree_bb	integer	1000	Ultrafast bootstrap replicates
--iqtree_alrt	integer	1000	SH-like approximate likelihood ratio test replicates
--iqtree_asr	boolean	false	Ancestral state reconstruction by empirical Bayes
--skip_phylogeny	boolean	false	Skip IQ-TREE execution in subworkflows

Used By

Subworkflows

• iqtree - Construct maximum likelihood phylogenetic trees from alignments.

Workflows

• pangenome - Pangenome analysis with optional core-genome phylogeny.
• snippy - Rapid haplotype variant calling and core genome alignment.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• IQ-TREE
  Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol. 32:268-274 (2015)

Source

View source on GitHub

Version

IQTREE:
    - iqtree: 3.1.1