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 or -?	Print help usage.
-s	Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format.
-st	Specify sequence type: BIN for binary, DNA for DNA, AA for amino-acid, NT2AA for converting nucleotide to AA, CODON for coding DNA and MORPH for morphology. This option is typically not necessary because IQ-TREE automatically detects the sequence type. An exception is -st CODON which is always necessary when using codon models (otherwise, IQ-TREE applies DNA models).
-q	Specify partition file in NEXUS or RAxML-style format for edge-equal partition model. That means, all partitions share the same set of branch lengths (like -q option of RAxML).
-spp	Like -q but each partition has its own rate (edge-proportional partition model).
-sp	Specify partition file for edge-unlinked partition model. That means, each partition has its own set of branch lengths (like -M option of RAxML).
-t	Specify starting tree for tree search. By default, IQ-TREE starts from 100 parsimony trees and BIONJ tree. The special option -t BIONJ starts tree search from BIONJ tree and -t RANDOM starts tree search from completely random tree.
-te	Like -t but fixing user tree. That means, no tree search is performed and IQ-TREE computes the log-likelihood of the fixed user tree.
-o	Specify an outgroup taxon name to root the tree. The output tree in .treefile will be rooted accordingly.
-pre	Specify a prefix for all output files. By default, the prefix is either the alignment file name (-s) or the partition file name (-q, -spp or -sp).
-seed	Specify a random number seed to reproduce a previous run. This is normally used for debugging purpose. By default, IQ-TREE draws a random number seed based on the current machine clock.
-v	Turn on verbose mode for printing more messages to screen. This is normally used for debugging purpose.