To run Evolmap, use the following command line:
java -jar -Xmx2g EvolMap1.1.jar options.txt

There is an example options file under other folder and fields are explained in the manual. New in version 1.1 is the processors=N option which is for multi-threading. Species fasta files must be next to the options file as specified with the name in tree plus the tag (e.g. .fa).

To run horizontal gene transfer detection, first run evolmap. Then specify a species and an ancestor for which the HGT events are to be detected using HGT.sh. Example run provided is used to detect HGTs in Amphimedon(sponge) of Archaea_Bacteria on the ancestor of all 21 species used in this analysis.

There are helper classes to detect GC content, GC content in first and third position of the transcripts, and find the origin of genes. These are currently executed manually in the source code.

For questions and suggestions, contact osakarya@yahoo.com