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

• -? or -h : Printing help usage.
• -s alignment_file : Input alignment in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format
• -st data_type : 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 partition_file : Edge-linked partition model (file in NEXUS/RAxML format)
• -spp partition_file : Like -q option but allowing partition-specific rates
• -sp partition_file : Edge-unlinked partition model (like -M option of RAxML)
• -t tree_file : Starting tree (default: 100 parsimony trees and BIONJ)
• -t BIONJ : Starting tree search from BIONJ tree
• -t RANDOM : Starting tree search from random Yule-Harding tree
• -te tree_file : Like -t but fixing user tree (no tree search performed)
• -o outgroup_taxon : Outgroup taxon name for writing .treefile
• -pre PREFIX : Using PREFIX for output files (default: aln/partition)
• -seed number : Random seed number, normally used for debugging purpose
• -v : Verbose mode, printing more messages to screen