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

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| -? or -h | Printing help usage | | -s | 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 | RANDOM | Starting tree (default: 100 parsimony trees and 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 | Using for output files (default: aln/partition) | | -seed | Random seed number, normally used for debugging purpose | | -v, -vv, -vvv | Verbose mode, printing more messages to screen |