Almost all my software projects are available at my Git repository. Some of the more popular or generally useful ones are:
DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the libary. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting â€œglueâ€ that assembles and drives such pipelines.
Forward-time spatially-explicit agent-based simulations of phylogeographic history over dynamic landscapes and environments.
A Python utility to monitor memory and other system resource usage of any running process (or any Python process invoked by it).
A prompt with attitude! Keep track of Git branch, SHA1 and repository status in glorious technicolor in your BASH prompt. Fully configurable in terms of color as well as whether to show long or short directory paths, hostnames, etc.
Simplified Git remote repository management.
Vim plugin for searching the local filesystem for files by name or content, using glob or regular expression patterns.
Vim plugin to search, index, and navigate buffer content using regular expression patterns.