Download AUGUSTUS from http://bioinf.uni-greifswald.de/augustus/binaries/ or from Github.
simplifyFastaHeaders.pl (a script for modifying fasta headers, will in the future be included in AUGUSTUS releases).
Download dFe-CRF (source code) from http://bioinf.uni-greifswald.de/ppi/ a commandline tool to predict protein-protein interaction interface residues given the target protein structure as a PDB-file.
An implementation of the Metropolis algorithm, a Markov-chain Monte Carlo method, to obtain the posterior distribution on matchings π proportional to M[1, π(1)] * M[2, π(2)] * ... * M[n, π(n)] for an input Matrix M with nonnegative entries. This program was used for our contribution to the 2015 Cricital Assessement of Genome Interpretation (CAGI).
Download source code and example: sample-matchings-0.1.tar.gz