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.

Option	Meaning
`-?` or `-h`	Printing help usage
`-s <alignment>`	Input alignment in PHYLIP/FASTA/NEXUS/CLUSTAL/MSF format
`-st <data_type>`	BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect)
`-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 <start_tree_file>	BIONJ
`-te <user_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, -vv, -vvv`	Verbose mode, printing more messages to screen