- The MSA project provides FPGA and GPU accelerated multiple sequence alignment.
- The PSODA project provides a phylogenetic search tool that reads the same data file format as PAUP*.
- MPSA2MDSA was developed to create DNA alignment benchmarks in order to test, rank, and improve current alignment algorithms. Thus far, the central focus on assessment of alignment applications has been on protein alignments; however, with a new "gold standard" of DNA alignments, it will be possible to better fill the need of good DNA alignment algorithms.
- Large Grain Alignment (LGA) is a software package that iterates through phases of multiple sequence alignment, phylogeny searches and calculating substitution matrices to provide a large grain optimization alignment that provides more refined alignments then packages like ClustalW and overcomes limitations in current optimization alignment packages such as POY.
- The Distributed Object Group Metacomputing Environment (DOGMA) project provides users with a distributed computing environment where computational science experiments can be executed on idle computers as well as clusters and supercomputers.
- TCS is a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks).
- Many data files have been assembled to test the software.
- The Drug Docking/Pathways undergraduate research group information is also available here.
- The Jumpstart phylogenetic search system allows you to reuse trees from previous searches in a current search.
- The ScaffoldScaffolder project is for haplotype-aware scaffolding of contigs. It also includes modules for solving the Contig Orientation Problem.
Please send suggestions and questions to Quinn Snell (firstname.lastname@example.org)