Starting with version 1.4.0, IQ-TREE implements the likelihood mapping approach ( Strimmer and von Haeseler, 1997) to assess the phylogenetic information of an input alignment. Iqtree -s example.phy -nt AUTO -mem 8G -pre myrun Iqtree-omp -s example.phy -nt AUTO -mem 8G -pre myrun Like above but write all output to myrun.* files: # For version <= 1.5.X Reconstruct a maximum-likelihood tree using at most 8 GB RAM and automatically detect the number of cores to use: # For version = 1.6.0, change iqtree-omp to just iqtree Reconstruct a maximum-likelihood tree given a sequence alignment file example.phy: iqtree -s example.phy
By default, IQ-TREE will try to not to exceed the computer RAM size. mem Specify maximal RAM usage, for example, -mem 64G to use at most 64 GB of RAM. This mode is automatically turned on when having more than 2000 sequences. safe Turn on safe numerical mode to avoid numerical underflow for large data sets with many sequences (typically in the order of thousands). Bu default: IQ-TREE will remove them during the analysis and add them in the end. keep-ident Keep identical sequences in the alignment. DEFAULT: OFF -quiet Silent mode, suppress printing to the screen. This is normally used for debugging purposes. DEFAULT: based on current machine clock -v Turn on verbose mode for printing more messages to screen. ntmax Specify the maximal number of CPU cores -nt AUTO is allowed to allocate DEFAULT: #CPU cores on the current machine -seed Specify a random number seed to reproduce a previous run. A special option -nt AUTO will tell IQ-TREE to automatically determine the best number of cores given the current data and computer. DEFAULT: either alignment file name ( -s) or partition file name ( -q, -spp or -sp) -nt Specify the number of CPU cores for the multicore version. DEFAULT: first taxon in alignment -pre Specify a prefix for all output files. o Specify an outgroup taxon name to root the tree. That means, no tree search is performed and IQ-TREE computes the log-likelihood of the fixed user tree. DEFAULT: 100 parsimony trees + BIONJ tree -te Like -t but fixing user tree. The special option -t BIONJ starts tree search from BIONJ tree and -t RANDOM starts tree search from completely random tree. t Specify a file containing starting tree for tree search.
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You can also use a genetic code like -st NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table). st NT2AA tells IQ-TREE to translate protein-coding DNA into AA sequences and then subsequent analysis will work on the AA sequences. Note that -st CODON is always necessary when using codon models (otherwise, IQ-TREE applies DNA models) and you also need to specify a genetic code like this if differed from the standard genetic code. This is only necessary if IQ-TREE did not detect the sequence type correctly. st Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences. s Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format. General options are mainly intended for specifying input and output files: Option Usage and meaning -h or -? Print help usage.
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