From ISOGG Wiki
Phylogeny programs are computer programs which allow the user to construct phylogenetic trees from genetic data. (Another word for a phylogenetic tree is a cladogram.) There are almost 400 free packages available. Phylogeny programs are used by population geneticists on large datasets but are sometimes also deployed by advanced Y-DNA and mtDNA project administrators.
The chief genetic genealogy benefit of phylogeny programs is the graphic portrayal of the genetic data. Diagrams may be useful in analysis and in presentations. They illustrate probable relationships among members of a genetic family and their relationships to a hypothesized "root" (the modal).
The popular programs used by genetic genealogists include:
- SAPP (Still Another Phylogeny Program). See the blog post from Maurice Gleeson L2 MHT - "difficult to place" people for a description of its use.
- List of phylogeny software, hosted at the University of Washington
- Tree building for Y-DNA projects by Dave Hamm. A comparison of tree-building packages.