- MEGA – Molecular Evolutionary Genetics Analysis package. It is a computer software for conducting automatic and manual sequence alignment and constructing phylogenetic trees.
- Phylip – It is a free package of programs for inferring phylogenies.
- PAML – A package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
- DAMBE – Software package for extensive Data Analysis in Molecular Biology and Evolution
- iTOL – Interactive Tree Of Life is an online tool for the display, annotation and management of phylogenetic and other trees.