implementations of the HGT algorithms
The HGT/FP algorithm of evolutionary tree reconstruction is implemented in C, and is available under the
GNU General Public License.
Download hgtfp.c, and tell me whether you like it (csuros AT iro.umontreal.ca).
(This is mostly legacy code...)
The Harmonic Greedy Triplets and Fast Harmonic Greedy Triplets algorithms,
along with some extra code for simulation experiments,
are implemented in Perl.
The implementation consists of several perl modules and some example
scripts. It is in a preliminary state, without extensive testing done.
If you want to download them, make sure to download all modules and
put them in the same directory, called fHGT (simplest is to
copy the directory structure at this location). Alternatively,
a gzipped tar archive (28k) can be downloaded,
which comprises all the files.
The modules are expected to be in a directory called fHGT,
relative to the script that wants to use them. A short
man-style documentation
is available for scripts.
The available modules are the following.
The scripts have been tested on Linux and MacOS (Classic). In order to run them on
Mac, you need MacPerl.
For Unix or Linux machines, don't forget to change the first lines to refer to
the location of perl on your system (usually /usr/local/bin/perl
on Unix, /usr/bin/perl on Linux). This can be done using
the setperl.csh csh script.
All scripts give
a description of their arguments when called with the -h
switch.
There are three file formats pertinent to these scripts. The sample file is an ``almost-Newick-compatible'' file for aligned sample sequences. (As of now, I haven't written a subroutine to read one in, but there is a script that generates a sample file. Huh!) The closeness file (more details in fHGT::Distance) is produced from a sample, it contains the pairwise closeness values between taxa (closeness is exp(-distance)). The tree file (more details in fHGT::Tree) is a Newick format description of a phylogeny.
There are some examples available using these scripts.