Please first download and install the binary for your platform. IQ-TREE takes as input a gamma of a binary option sequence alignment and will reconstruct an evolutionary tree that is best explained by the input data. The input alignment can be in various common formats. From the download there is an example alignment called example.
Bird form a separate sister clade. Here the tree is drawn at the outgroup Lungfish which is more accient than other species in this example. This prevents output files being overwritten when you perform multiple analyses on the same alignment within the same folder. NOTE: If you use model selection please cite the following paper:S. IQ-TREE supports a number of codon models. 6 we provide a new option -bnni to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. The standard nonparametric bootstrap is invoked by the -b option:iqtree -s example.
G -b 100 -b specifies the number of bootstrap replicates where 100 is the minimum recommended number. The output files are similar to those produced by the UFBoot procedure. To perform this test, run:iqtree -s example. G -alrt 1000 -alrt specifies the number of bootstrap replicates for SH-aLRT where 1000 is the minimum number recommended. Other branches appear to be well supported.
IQ-TREE can utilize multiple CPU cores to speed up the analysis. A complement option -nt allows specifying the number of CPU cores to use. Note that for old IQ-TREE versions iqtree to iqtree-omp for all commands below. G -nt 2 Here, IQ-TREE will use 2 CPU cores to perform the analysis.