Research and Analysis
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 “pipeline” that assembles and drives such pipelines.
Ginkgo is a forward-time spatially-explicit agent-based simulations of phylogeographic history over dynamic landscapes and environments.
Teaching and Learning
System and Utilities
promptitude is a shell 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.