phylofriend

Phylofriend

Phylofriend’s main purpose is to calculate genetic distances from Y-chromosome STR values. The results can be used as input for the PHYLIP program to create phylogenetic trees.

Phylofriend supports all 587 STR markers that are reported by YFull (March 2018).

Documentation

• User Guide
• Source Code

How to Create a Phylogenetic Tree

1. Copy persons’ data from a Family Tree DNA project website into a spreadsheet. If the Y-STR values do not appear properly try inserting them into the spreadsheet as unformatted text.
2. Save the spreadsheet in CSV (comma separated values) format, for example persons.csv.
3. Start a terminal or command line interpreter and go to the directory where you stored persons.csv.
4. Create a matrix of genetic distances by typing phylofriend -personsin persons.csv -phylipout infile.
5. Use the PHYLIP program to create a tree in Newick format with /usr/lib/phylip/bin/kitsch. You will need to answer some questions. Usually the default values are good enough. The results will be two text files, one named outtree which contains the tree in Newick format and another one named outfile which contains a more human readable description.
6. Create an image of the tree by typing /usr/lib/phylip/bin/drawgram. Use outtree as the input file name. The resulting tree will be stored in a file named plotfile.