Software

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Software on Github
  • FastNN (Fast Neighbor-Net) is a fast and memory efficient Java 7 command-line implementation of Neighbor-Net, a popular phylogenetic split network algorithm by Bryant and Moulton.  The output can be rendered in SplitsTree4It features multithreading and new faster (but less accurate) relaxed and random search heuristics. A Java JAR is provided for convenience by clicking on the download arrow.
  • BisPin is a Python 2.7 program that uses BFAST to map bisulfite-treated short DNA reads to a reference genome.  It supports the hairpin construction strategy and rescores ambiguously mapped reads.  Its default alignment scoring function is biologically motivated.
  • PorterTools is a collection of Python 2.7 scripts for processing biological sequence data that have been developed over the course of my research.  They are provided for reference.

 

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FastNN.v.0.3.5.tar
(1105k)
Jacob Porter,
Nov 2, 2015, 1:10 PM