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). Web based interface. Takes a plain text data file (*.txt) as input. which contains the STR results, SNPs, and Genealogies for SAPP to use in building the phylogenetic tree. See the blog post from Maurice Gleeson L2 MHT - "difficult to place" people for a description of its use.
- MEGA Software for generating Phylogenetic and Network Tree graphs from the PHYLIP data.
The above phylogeny programs often require data to be converted into a format used as input. For example, in the PHYLIP package contains software that requires Genetic Distance input for Kitsch, the DNAML program requires ATGC data format, and other packages can require frequency data, newick tree format, etc. The following programs convert data for use with phylogeny software.
- Phylofriend Open source program that calculates genetic distances from Family Tree DNA projects to create phylogenetic trees with PHYLIP. It accepts Y-DNA STR data and YFULL data for building phylogenetic trees, etc.
- Dean McGee's Y-DNA Utility Option for FTDNA mode, up to Y-DNA111 markers for Genetic Distance and TMRCA tables. It can output to PHYLIP and Fluxus for building phylogenetic trees, etc.
- FT2DNA Dave Hamm's utility to convert Family Tree DNA's Y-chromosome repeat data format into raw code (i.e.: ATGC) for analysis by other utilities.
- FT2PHY Dave Hamm's tool for the conversion of FTDNA repeat data format files into ATGC format files for use with PHYLIP compatible packages, such as DNAML. This program uses input that is compatible with Dean McGee's Y-DNA Utility.
- Autosomal DNA Half Life Equation for autosomal DNA (atDNA) to calculater Genetic Distance (cousin level) calculations for each segment. Can be input into an Excell spreadsheet or calculated within a program. Can also be modified for segment sums, etc. The output from the equation can be used as Genetic Distance for the Kitsch program within the PHYLIP package. Multiple trees can be combined with the TreeDist program within the PHYLIP package. Works with individual segments in cMs or use the modified equation for total sums in cMs.
- 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.
- Instructions for creating TMRCA phylogenetic charts from DNA information