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_file`	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`	Verbose mode, printing more messages to screen