porthoDom is a program for orthology detection using protein domains as a filtering step. It is meant to be used with proteinOrtho.
The porthoDom software with detailed installation instruction can be downloaded at this link: porthodom.tar.bz2
The git repository with the latest code development can be found here: https://zivgitlab.uni-muenster.de/ag-ebb/subsidiary_projects/porthodom
The Pfam 27 domain pairwise similarity matrix can be found here: matrixPfam27_bin_1.dat.gz
If you used porthoDom in your project please cite our publication:
Bitard-Feildel T, Kemena C, Greenwood JM, Bornberg-Bauer E, Domain similarity based orthology detection, BMC Bioinformatics. BMC Bioinformatics. 2015 16:154. doi: 10.1186/s12859-015-0570-8.