balabanmetin

uDance

apples

distance based phylogenetic placement

misa

mixed sample analysis

snakemake-tutorial2

Short snakemake tutorial

misa-data

Data & Scripts used in paper "Phylogenetic double placement of mixed samples"

apples2-data

uDance-legacy

bac10

balabanmetin.github.io

compareTrees

The MicrobesOnline tree comparison tool

cpython

The Python programming language

cse282

FastLoo

Subquadratic leave-one-out outlier detection via a APPLES-2

gg2_protocols

hatchet

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

hgt_simulation

mainlines

quickly reduce MSA size by removing low-diversity sequences

newCNbulk

raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible

reference_flow

Reducing reference bias using multiple population reference genomes

sepp-1

Ensemble of HMM methods (SEPP, TIPP, UPP)

SkmerExtended_Tool

snakemake-tutorial

tk4-evol-sim

Simulates two genomes that evolve under TK4 model of evolution

tools

Sorts of tools

tools-1

A collection of command-line tools I wrote to make various repetitive tasks more convenient

udance-data

Data for uDance paper

uDance-figures

R script and data

wol2-16k-data

yeast-genomes

genomes of pure and hybrid yeast species & gold standard phylogeny of pure species