Our software is hosted on the evolbioinf repo, here are four highlights:

  • phylonium: Fast distance computation between genome sequences for phylogeny reconstruction; paper.

  • fur: Find unique regions for marker discovery from whole microbial sequences; paper.

  • Biobox: Collection of some 50 bioinformatics tools used in textbook on sequence analysis on the command line. They cover alignment, compression, exact matching, plotting of graphs, trees, and networks, manipulation of FASTA sequences, manipulation of phylogenies, and statistics.

  • Neighbors: Collection of tools for finding samples of target and neighbor genomes from the NCBI taxonomy, and for sorting them into phylogenetic targets and neighbors.