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IQ-TREE3 container

Main tool : iqtree3

Full documentation: https://iqtree.github.io/doc/

| Efficient and versatile phylogenomic software by maximum likelihood

Example Usage

An example phylip file (IQ-TREE2 also supports other file formats such as FASTA, NEXUS, CLUSTALW)

7 28
Frog       AAATTTGGTCCTGTGATTCAGCAGTGAT
Turtle     CTTCCACACCCCAGGACTCAGCAGTGAT
Bird       CTACCACACCCCAGGACTCAGCAGTAAT
Human      CTACCACACCCCAGGAAACAGCAGTGAT
Cow        CTACCACACCCCAGGAAACAGCAGTGAC
Whale      CTACCACGCCCCAGGACACAGCAGTGAT
Mouse      CTACCACACCCCAGGACTCAGCAGTGAT

Can be aligned with the following command:

iqtree3 -s example.phy -redo

Helpful parameters include:

  • -m MFP: Uses ModelFinder Plus to perform ModelFinder and use the selected model for remaining analysis.
  • -st: Used to swap from a DNA model to another sequence type model.
  • -mem: Restricts memory usage
  • -nt AUTO: Automatically determine the best number of cores given the current data and computer.