- See my gitub page to see all my publicly available software programs.
Some of these are from my days as a graduate student advised by Tandy Warnow
- 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).
- UPP: Ultra-large alignments using Phylogeny-aware Profiles (uses SEPP).
- 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
- I also work on and contribute code to SATé.
- Also checkout the following github pages from students in the lab.
- Uyen Ma:
Refer to this site for most of the datasets we have published through years.