Command Reference

Table of Contents

• Command line interface
• General options

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 or -spj	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. The special option -t BIONJ starts tree search from BIONJ tree and -t RANDOM starts tree search from completely random tree. DEFAULT: IQ-TREE starts from 100 parsimony trees plus BIONJ 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. DEFAULT: first taxon in alignment
-pre	Specify a prefix for all output files. *DEFAULT: either alignment file name (-s) or 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. DEFAULT: based on current machine clock
-v	Turn on verbose mode for printing more messages to screen. This is normally used for debugging purpose. DFAULT: OFF

Tree search parameters

Option	Usage and meaning
-numpars	Specify number of initial parsimony trees. DEFAULT: 100
-toppars	Specify number of top parsimony trees of initial ones for further search. DEFAULT: 20
-numcand	Specify number of top candidate trees to maintain during tree search. DEFAULT: 5
-sprrad	Specify radius for subtree prunning and regrafting parsimony search. DEFAULT: 6
-pers	Specify perturbation strength (between 0 and 1) for randomized nearest neighbor interchange (NNI) DEFAULT: 0.5
-allnni	Turn on more thorough NNI during tree search. It means that IQ-TREE will consider all possible NNIs instead of only those in the vicinity of previously applied NNIs. DEFAULT: OFF
-numstop	Specify number of unsuccessful iterations to stop. DEFAULT: 100
-n	Specify number of iterations to stop. This option overrides -numstop criterion.