Mathematical and Computational Biology
in the Department of Mathematics at UC Berkeley

• AMAP Protein multiple alignment
• FSA Fast statistical alignment
• GENEMAPPER Reference based gene annotation
• MAVID Multiple alignment of large genomic sequences
• MERCATOR Homlogy mapping
• MJOIN Neighbor joining with subtree weights
• riskPoly Computation of risk polynomials
• SLAM Pairwise simultaneous alignment and gene finding
• SLIM Minimum network design for optimizing the search space for pair hidden Markov models
• TangleSolve Analysis and visualization of DNA recombination mechanisms
• treeSVD Building phylogenetic trees and testing splits using singular value decomposition

DNA

There is a great satisfaction in building good tools for other people to use. (Freeman Dyson)