Siavash Mirarab

ASTRAL. Accurate Species TRee ALgorithm

pasta. PASTA (Practical Alignment using SATe and Transitivity)

sepp. Ensemble of HMM methods (SEPP, TIPP, UPP)

1kp. Data and scripts used in the oneKP capstone analyses

FastSP. Software for comparing two (very large) alignments efficiently

binning. Code for statistical binning and related scripts

tutorials.

sepp-refs.

DynaDup. Software to Estimate Species Tree by minimizing Duplication and Loss

skimming_scripts. scripts for preprocessing/analysis of genome skim data

mrpmatrix. builds a MRP (Matrix Representation with Parsimony) matrix on huge input files quickly

chr4avian. WDL

mirarablab.

global. Java

GORG-LGT. Mathematica

avian-indels. Code and data from the indel data

multi-locus-bootstrapping. Creates sets of bootstrap replicates for multi-locus bootstrapping