ABSTRACT
There are over 500 phylogenomic and phylogenetic programs given on Joe Felsenstein’s comprehensive list of programs. Programs for phylogenetic analysis can be found on the Web, and this chapter lists dozens of programs and how to access them. Programs for phylogenetic analysis can be used online or downloaded for desktop use. Dozens of programs exist for use in the comparative method, and we mention over 20 of them in this chapter and how to download them. There are several all-purpose/full-service platforms that exist for phylogenomic analysis.
