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Summary: We make available a large cross-comparison for 16 of the completely sequenced genomes and additional eukaryotic genes. The alignments were performed at the protein level using liberal similarity bounds in order to capture as many significant alignments as possible. This dataset will be updated as new genomes become available.

Motivation: We announce the availability of the second release of Darwin v. 2.0, an interpreted computer language especially tailored to researchers in the biosciences. The system is a general tool applicable to a wide range of problems., Results: This second release improves Darwin version 1.6 in several ways: it now contains (1) a larger set of libraries touching most of the classical problems from computational biology (pairwise alignment, all versus all alignments, tree construction, multiple sequence alignment), (2) an expanded set of general purpose algorithms (search algorithms for discrete problems, matrix decomposition routines, complex/long integer arithmetic operations), (3) an improved language with a cleaner syntax, (4) better on-line help, and (5) a number of fixes to user-reported bugs., Availability: Darwin is made available for most operating systems free of char ge from the Computational Biochemistry Research Group (CBRG), reachable at http://chrg.inf.ethz.ch., Contact: darwin@inf.ethz.ch