Software listed below for download is software used in research papers as indicated for each entry. These codes were not developed as tools for the general community -- they are research codes and as such do not have pretty interfaces or documentation (other than the research papers that use them), nor are they guaranteed to compile and run on platforms other than current Linux systems.
 

• Xiuwei Zhang, Maryam Zaheri, Bernard M.E. Moret. Using phylogenetic relationships to improve the inference of transcriptional regulatory networks, Proceedings of the First International Conference on BioMedical Engineering and Informatics (BMEI2008), 1:186-193. PDF, Download source code
• Xiuwei Zhang and Bernard M.E. Moret. Boosting Inference of Regulatory Networks Using a Phylogenetic Approach, Lecture Notes in Computer Science (8th Workshop on Algorithms in Bioinformatics, WABI2008), 5251: 245-258. PDF, Download source code
• The source code of refinement algorithms with extended network evolution model which takes into account gene duplications and losses: Download source code
• DomML - Ab initio prediction of protein domains based on maximum likelihood. An online version is available here.
• FluRF - An automated flu virus reassortment finder based on phylogenetic trees: Download source code
• Nishanth Ulhas Nair, Avinash Das Sahu, Philipp Bucher, Bernard M.E. Moret. ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries, PLoS ONE, 2012, Download source code.
  Relevant output as modification sites can be seen in UCSC genome browser here.
• TIBA: Tree Inference with Bootstrap Analysis