We have written and maintain several software packages and web servers to support our research and make algorithms we developed available to the community.
- Lyne (collaboration with the Kostka Lab)
Lyne is an R package implementing continuous time Markov models for modeling the dynamics of epigenetic marks (like DNA methylation) on cell lineage trees.
ProteinHistorian is an integrated system (web server and command line programs) for predicting protein ages and identifying enrichment for proteins of different ages in protein sets of interest. Over thirty eukaryotic species are currently supported. Other phenotypic data can also be uploaded to combine with the protein age analysis.
ConCavity predicts small molecule ligand binding sites in proteins by combining information from evolutionary conservation and protein 3D structure. Pre-computed predictions and visualizations are available for most structures in the PDB and a command line version is available to enable analysis of new structures.
GroupSim predicts protein residues likely to determine functional specificty from multiple sequence alignments of protein famililies.
- Scoring Evolutionary Conservation Using Jensen-Shannon Divergence
This web server and program score the evolutionary conservation of positions in a multiple sequence alignment of proteins using the Jensen-Shannon divergence method. This approach is very fast and has performed well in several independent evaluations. The program also implements several other popular conservation estimation methods.