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IQTREE infers phylogenies from multiple sequence alignments.
If you found IQTREE useful, please cite IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Minh et al. 2020, Molecular Biology and Evolution. doi: 10.1093/molbev/msaa015.
To run IQTREE, user's must provide a minimum a multiple sequence alignment. This workflow conducts automated substitution matrix model testing. Specify output prefixes and the number of ultrafast bootstrap approximations (or UFBoot) to run.