Process the HiCPro results of inter-chromosome matrix, and make it fit to hicPlotter input.

Simple lightweight installer for R packages from GitHub without external dependencies

BuffaloAssemblyScripts

Whole genome alignments using LastZ software in vertebrate species. Code (1) drives embarrassingly parallel execution of commands, (2) merge output into sensible formats and (3) provides ways to dr…

Code and data for the article “Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 34 primate species”

The general workflow for processing UCE data that I use

code for LRR-RLK evolution paper

De novo SNV analysis pipeline

Comparative genomics project examining the role of convergent evolution in the independent origin of viviparity in Cyprinodontiformes. Steps include, aligning, chaining, netting, multiple sequence …

Scripts to recreate figures from the scmap paper

Key codes for Towards a developmental biology of superorganisms: reconstructing the canalized trajectories of caste differentiation in ants

Scripts for studying the evolution of immune genes across birds.

examination of genome size across all kingdoms

R package for the reproducible detection of synteny blocks using genetic map data

TransMap is an analysis pipeline for cross-species comparative transcriptome expression analyses.

Genome Evolution Lecture for Phylogenomics Workshop

Scripts and data for "A cautionary tale on the use of branch-site models to detect convergent positive selection"

Codes for comparative ant brain transcriptomes

A repository of scripts supporting the manuscript "Marsupial genomes from two continents reveal clues to the evolution of suicidal reproduction"

Analysis from "Comparative transcriptomics of social insect queen pheromones" (Nature Comms, 2019)

Python and R scripts used in analyses of whole genome duplication events and diversification

This repository contains a custom R script to plot Circos plots using Circlize to identify synteny between linkage groups and chromosomes in a reference genome

Rapidly Evolving Long Exon Capture

Code used in 2015 ARJ paper "Documented Anomaly in Recent Versions of the BLASTN Algorithm and a Complete Reanalysis of Chimpanzee and Human Genome-Wide DNA Similarity Using Nucmer and LASTZ"

core model training and combining for the limb enhancer genie (LEG)

Pipeline and scripts for maize NAM line annotation and analysis