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 change iqtree to the actually path to the executable or read the Quick start guide.

General options

General options are mainly intended for specifying input and output files:

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 a file containing 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: 100 parsimony trees + 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

The new IQ-TREE search algorithm (Nguyen et al., 2015) has several parameters that can be changed with:

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 and slower NNI 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.

NOTICE: While the default parameters were empirically determined to work well under our extensive benchmark (Nguyen et al., 2015), it might not hold true for all data sets. If in doubt that tree search is still stuck in local optima, one should repeat analysis with at least 10 IQ-TREE runs. Moreover, our experience showed that -pers and -numstop are the most relevant options to change in such case. For example, data sets with many short sequences should be analyzed with smaller perturbation strength (-pers) and larger -numstop.

Ultrafast bootstrap parameters

The ultrafast bootstrap (UFBoot) approximation (Minh et al., 2013) has several parameters that can be changed with:

Option	Usage and meaning
-bb	Specify number of bootstrap replicates (>=1000).
-wbt	Turn on writing bootstrap trees to .ufboot file. DEFAULT: OFF
-wbtl	Like -wbt but bootstrap trees written with branch lengths. DEFAULT: OFF
-nm	Specify maximum number of iterations to stop. DEFAULT: 1000
-bcor	Specify minimum correlation coefficient for UFBoot convergence criterion. DEFAULT: 0.99
-nstep	Specify iteration interval checking for UFBoot convergence. DEFAULT: every 100 iterations
-beps	Specify a small epsilon to break tie in RELL evaluation for bootstrap trees. DEFAULT: 0.5

Nonparametric bootstrap

The standard nonparametric bootstrap (Felsenstein, 1985) can be run with:

Option	Usage and meaning
-b	Specify number of bootstrap replicates (recommended >=100). This will perform both bootstrap and analysis on original alignment and provide a consensus tree.
-bc	Like -b but omit analysis on original alignment.
-bo	Like -b but only perform bootstrap analysis (no analysis on original alignment and no consensus tree).