Command Reference

Command line interface

iqtree -s <alignment> [OPTIONS]

Assuming that IQ-TREE can be run by simply entering iqtree. If not, please read the Quick start guide.

General options

Option	Usage and meaning
-h	Printing help usage.
-s	Input alignment in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format.
-st	Specifying sequence type with BIN (binary), DNA, AA (amino-acid), NT2AA (converting NT to AA), CODON, MORPH (morphology). By default IQ-TREE automatically detects the sequence type.
-q	Edge-linked partition model (file in NEXUS/RAxML format).
-spp	Like -q option but allowing partition-specific rates.
-sp	Edge-unlinked partition model (like -M option of RAxML).
-t	Starting tree for tree search instead of the default of 100 parsimony trees and BIONJ. -t BIONJ starts tree search from BIONJ tree. -t RANDOM starts tree search from random Yule-Harding tree.
-te	Like -t but fixing user tree (no tree search performed).
-o	Outgroup taxon name for writing .treefile.
-pre	Using PREFIX for output files (default: aln/partition).
-seed	Random seed number, normally used for debugging purpose.
-v	Verbose mode, printing more messages to screen.