Our software is hosted on the Github site evolbioinf, where we keep over 60 public repositories. These fall into two categories, programs and libraries.

Programs

Our programs are concentrated on four topics, genetic marker discovery, estimation of evolutionary distances and tools for sequence analysis. Most of them are written in the literate programming style to address human readers rather than machines. The majority of our programs run under the Unix command line, but there are exceptions like our website for visualizing the NCBI taxonomy, Vitax. There’s also a dedicated Docker container for testing our command line tools.

  • Marker Discovery
    • Fur: Find Unique Regions. Given a sample of target genomes and a sample of closely related neighbor genomes, find all regions common to the targets that are absent from the neighbors. These regions make excellent starting material for constructing genetic markers.
    • Neighbors: Software for finding target and neighbor genomes, that is, the input for Fur. Neighbors comes with a dedicated web server, Never, and a tool for visualizing the taxonomy of sequenced life, Vitax.
    • Prim: Software for constructing and testing diagnostic PCR primers, that is, for testing the output of Fur.
  • Evolutionary Distances
    • andi: Pairwise anchor distances between closely related DNA sequences. For a much faster version, see phylonium.
    • phylonium: Pairwise anchor distances between closely related DNA sequences. For a slightly more accurate version, see andi.
  • Sequence Analysis
    • Biobox: Collection of some 60 bioinformatics tools used in the textbook Bioinformatics for Evolutionary Biologists. A Problems Approach by Bernhard Haubold and Angelika Börsch-Haubold. The book is on sequence analysis on the Unix command line and covers alignment, compression, exact matching, plotting of graphs, trees, and networks, manipulation of FASTA sequences, manipulation of phylogenies, and statistics.
    • bioGrep: A grep-like tool for biological sequences.
    • ms2dna: Convert haplotypes generated with the program ms to DNA sequences.
  • Data simulation
    • stan: Simulates targets and neighbors genomes under a coalescent model.
  • Software Testing
    • Mix: Docker container that servers as a Minimum Unix Box, which we use as a defined starting point for testing our programs and finding their dependencies.

Libraries

Here are three libraries that are typical of our work and that we use a lot.

  • esa: Enhanced suffix array.
  • fasta: Dealing with FASTA-formatted sequences.
  • nwk: Handle phylogenies in Newick format.