Please first download and install the binary for your platform. IQ-TREE binary option introduction as input a multiple 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.