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Welcome to the bsrTools wiki!

This project aims to provide a set of tools that will facilitate clustering of fragmented protein coding sequences (CDS) using a graph with edges weighted by bit score ratios. The general workflow is very similar to the one used by OrthoMCL, which introduced practical solutions to many subproblems associated with clustering homologous CDS. OrthoMCL was designed to cluster full-length CDS however, and the implementation seems more focused on supporting the associated web service, rather than end users who would prefer to download and run the software themselves.

I have come to value a software development philosophy that favors the creation of simple tools that can be combined in powerful ways, rather than the creation of complex tools that have been optimized for specific tasks. It is my hope that users familiar with *nix command line working environments will find bsrTools relatively approachable. I will attempt to follow standard Python and *nix conventions, as I have come to know them, and will also try to find time to provide additional documentation for those who are new to both.