Datasets

Refer to this site for most of the datasets we have published through years.

Software

  • See my gitub page to see all my publicly available software programs. These are most from my days as a graduate student advised by Tandy Warnow, but some have been updated by my lab.
    • ASTRAL: Species tree estimation from unrooted gene trees using a quartet-based approach (consistent under multi-species coalescent process and hence useful for handling gene tree incongruence caused by ILS).
    • Other developers: Chao Zhang, Maryam Rabiee, John Yin, and Erfan Sayyari.
    • PASTA: Software for alignment and tree estimation on very large datasets (thousands to hundreds of thousands of sequences). This is a new version of SATé, and the code is heavily based on the SATé code.
    • Other developers: Uyen Mai, Kodi Collins
    • SEPP: Software for fast phylogenetic placement based on SATe decomposition - useful for metagenomic analyses
    • Other developers: Nam Nguyen, Mike G Nute, Stefan Janssen
    • TIPP: Taxonomic identification and taxonomic profiling of metagenomic samples (uses SEPP).
    • Other developers: Nam Nguyen, Mike G Nute
    • UPP: Ultra-large alignments using Phylogeny-aware Profiles (uses SEPP).
    • Other developers: Nam Nguyen, Uyen Mai
    • FastSP: Fast and Memory efficient software for comparison of multiple sequence alignments (computes SP-FN and TC scores)
    • Statistical binning: the code to perform statistical binning
    • Misc: a patchwork of scripts for phylogenetics and MSA that may be useful to others
  • Also checkout the following github pages from students in the lab.