R package to draw syntenic plots in 3 different styles

Genomic plot in trellis layout

Scripts to recreate figures from the SC3 paper

A package to manage and compile functional trait data into predefined templates

An R framework for phylostratigraphy

Genome alignment and synteny plots

Software Package for Transcription Factor Binding Site (TFBS) Analysis

A quick user guide for de novo transposable element (TE) library generation and TE screening. Utilising; the Extensive de novo TE Annotator (EDTA), DeepTE, RepeatMasker and RM_TRIPS.

Calculate and plot distributions of genomic ranges

Codes for calculating delta, a phylogenetic analog of the Shannon entropy for measuring the degree of phylogenetic signal between a categorical trait and a phylogeny.

plot genome alignment synteny

Analysis tools for longevity research

repository of scripts for comparative transcriptome analysis

ChIP-seq and ATAC-seq analysis

Two methods for mapping and visualizing associated data on phylogeny using ggtree

Nucmer from Mummer3 followed by ggplot for nicer and more customisable genome alignment plots.

AnceTran2.0: R package for transcriptome evolution analysis based on RNA-seq expression data or ChIP-seq TF-binding data

This is a phylogeny workflow for batch submission to HPC cluster built with Slurm queue manager

Rattlesnake venom population genomics

Analysis of the evolutionary stability of topologically associating domains in different vertebrate species.

This folder contains the testing empirical data and R code for CorrTest.

Scripts accompanying publication Cagan, Baez-Ortega et al., 2022