WinBioinfTools: Bioinformatics tools for windows cluster

Open source bioinformatics tools running under MS Windows are rare to find, and those running underWindows HPC cluster are almost nonexisting, in spite of the fact that Windows is the most popular operating system. Therefore, we introduce WinBioinfTools, an open source toolkit containing a number of bioinformatics tools running under Windows High Performance Computing Server 2008. The current version contains three programs for biological sequence analysis: 1) CoCoNUT for pairwise genome comparison, 2) WinBLAST for biological database search, and 3) WinPSA for global pairwise sequence alignment. We show how the Linux/Unix components of these programs were ported to run underWindows.We also demonstrate by experiments the advantage of using a computer cluster compared to a single machine, highlighting the benefits of using the Windows HPC Cluster 2008. Furthermore, we compare the performance of WinBioinfTools on the Windows- and Linux Cluster. © 2009 IEEE.