See my gitub page to see all my publicly available software programs.

  • 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).

  • 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.

  • SEPP: Software for fast phylogenetic placement based on SATe decomposition - useful for metagenomic analyses

  • TIPP: Taxonomic identification and taxonomic profiling of metagenomic samples (uses SEPP).

  • FastSP: Fast and Memory efficient software for comparison of multiple sequence alignments (computes SP-FN and TC scores)

  • I also work on and contribute code to SATé.

Also checkout the following github pages from current students in the lab.