jhh130910

protein-GO-term-annotation

Book-PDF-Free

CAFE

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

variant-call

A shell script which implements GATK pipeline for variant calling.

beast2

Bayesian Evolutionary Analysis by Sampling Trees

books

daily_py

save daily code

plot_Demo_code

code-test

cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js

DensiTree

Automatically exported from code.google.com/p/densitree

EMBLmyGFF3

An efficient way to convert gff3 annotation files into EMBL format ready to submit.

github_logos

golang

HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

incubator-echarts

A powerful, interactive charting and visualization library for browser

iterm2-zmodem

Automatic ZModem support for iTerm 2

MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

miRNA-analysis-pipeline

MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

pasta

PASTA (Practical Alignment using SATe and Transitivity)

plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase).

plotly.py

An open-source, interactive graphing library for Python :sparkles:

pycharm

sphinx-github-ReadsTheDoc

Stacks_pipeline

An automated and repeatable workflow for processing ddRADseq data using tools including Stacks. Goes from sequencer files to input files for commonly used phylogenetic/phylogeography programs.

timpo

VCF2Dis

VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

workshop-popgenome

Tutorial about R package PopGenome