As a bioinformatics research lab, we consider the development and dissemination of methods, software, and resources to be an integral part of our activities.
- The Orthologs Matrix (OMA) project: The OMA (“Orthologs MAtrix”) project is a method and database for the inference of orthologs among complete genomes. The distinctive features of OMA are its broad scope and size, high quality of inferences, feature-rich web interface, availability of data in a wide range of formats and interfaces, and frequent update schedule of two releases per year. OMA classifies genes from approximately 2,000 species into families of orthologs.
- Phylo.io is a web-based phylogenetic tree visualization tool with powerful side-by-side comparison features.
- ALF is a tool to generate simulated gene or genome sequences. Although it supports many models of sequence evolution, the intuitive interface with several sets of default parameters makes it very easy to use. It is available both as a downloadable version and web interface. ALF simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs.
- Orthology Benchmark Service is a web-based server to assess the quality of ortholog predictions. It aims at simplifying and standardizing orthology benchmarking. And for the users, the benchmarks provide a way to identify the most effective methods for the problem at hand.
- swps3 is a highly optimized Smith-Waterman implementation for x86 and IBM Cell B.E. architectures. swps3 is currently one of the fastest implementation of a vectorized Smith-Waterman on x86 and the Cell/B.E.
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