Tools

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.
  • Uyen Mai:
    • Minimum Variance (MV) rooting: also includes an efficient implementation of the MP rooting
    • tripVote
    • TreeShrink: a tool for detecting extremely and suspiciously long branches on a (set of) tree(s)
    • LogDate: dating phylogenies using log transformation
    • MD-Cat: dating phylogenies using categorical rates
  • Erfan:
    • DISTIQUE: species tree inference using distance
    • DiscoVista: A visualization tool for showing discordance among gene trees and species trees
    • TADA: Data augmentation for learning from microbiome compositional data
  • Niema:
    • FAVITES: Simulation of HIV on social networks
    • Dual-birth: a set of scripts to work with the dual-birth model
    • TreeCluster: A tool for clustering leaves of phylogenetic tree in a principled way
    • ProACT
  • Maryam Rabiee
    • INSTRAL: A tool that extends ASTRAL for phylogenetic placement
    • Constrained ASTRAL: A tool that extends ASTRAL for constrained tree search
    • SODA
    • QuCo
  • Metin Balaban
    • APPLES
    • MISA
    • uDance
  • Chao Zhang
    • Astral-Pro
    • TAPER
    • Next generation of ASTRAL-like tools, including A-Pro-2, wASTRAL, and CASTER
  • Yueyu Jiang
    • DEPP
  • Eleonora Rachtman
    • CONSULT
  • Shahab Sarmashghi
    • Skmer
    • RESPECT
  • Shayesteh Arasti
    • qSPR
    • TCMM
  • Ali Osman Berk Şapcı
    • CONSULT-II: Accurate taxonomic classification and abundance profiling using locality-sensitive hashing.
    • KRANK: Memory-bound k-mer selection for large evolutionary diverse reference libraries.
  • Yasamin Tabatabee
    • CASTLES