iqtree
Tags: phylogeny maximum-likelihood tree bootstrap model-selection run-scope
Construct maximum likelihood phylogenetic trees from alignments.
This subworkflow uses IQ-TREE to build maximum likelihood phylogenetic trees from multiple sequence alignments. IQ-TREE implements fast and effective stochastic algorithms for phylogenetic inference, including automatic model selection via ModelFinder. It produces phylogenetic trees with bootstrap support and various supplementary files for tree visualization and analysis.
Take
alignment: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
aln | Multiple sequence alignment in FASTA format |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
No sample-scope outputs.
run_outputs
| Output | Description |
|---|---|
aln | Input multiple sequence alignment (passed through) |
nwk | Maximum-likelihood phylogenetic tree in Newick format |
supplemental | Detailed report, distance matrix, and model parameters |
Module Composition
This subworkflow calls the following modules:
- iqtree - Efficient phylogenomic inference using Maximum Likelihood.
Used By
This subworkflow is used by the following 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)