Main tool : iqtree2
Full documentation: https://github.com/rrwick/Polypolish/wiki
| Efficient and versatile phylogenomic software by maximum likelihood
An example phylip file (IQ-TREE2 also supports other file formats such as FASTA, NEXUS, CLUSTALW)
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Frog AAATTTGGTCCTGTGATTCAGCAGTGAT
Turtle CTTCCACACCCCAGGACTCAGCAGTGAT
Bird CTACCACACCCCAGGACTCAGCAGTAAT
Human CTACCACACCCCAGGAAACAGCAGTGAT
Cow CTACCACACCCCAGGAAACAGCAGTGAC
Whale CTACCACGCCCCAGGACACAGCAGTGAT
Mouse CTACCACACCCCAGGACTCAGCAGTGAT
Can be aligned with the following command:
iqtree2 -s example.phy --redo