PhyD*: Fast NJ-like algorithms to deal with incomplete distance matrices.

Criscuolo A., Gascuel O.
BMC Bioinformatics. 2008, Mar 26;9:166.

Please cite THIS paper if you use PhyD*.

Running PhyD*

PhyD* uses a PHYLIP-like interface (Felsenstein, 1993). The user is asked for the name of the input file. This file contains one (or several) distance matrix in PHYLIP format (lower triangular or square). A missing entry must be written -99.0. Binary values (Subreplicate option) may be associated just after each matrix entry; the 0 value indicates a missing entry and the 1 value indicates a non-missing entry. Comments can be written inside the input file if the line begins with the '%' character.

Here is an example of input.d file containing square distance matrices:
PhyD* matrice example
The same three distance matrices with both lower triangular and subreplicate formats:
PhyD* matrice example
PhyD* outputs the phylogenetic tree(s) (in NEWICK format) inside a file called output.t.

To run PhyD* with LINUX, use the command:
java -jar PhyDstar.jar
To run PhyD* with WINDOWS, double-click on win_PhyDstar.bat.

PHYLIP-like interface

A PHYLIP-like menu display the various options:

PhyD* PHYLIP-like interface