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adapterremoval

This program was developed to remove residual adapter sequences from next generation sequencing reads. The program handles both single end and paired end data.

adegenet

adegenet: a R package for the multivariate analysis of genetic markers

beast2

Bayesian Evolutionary Analysis by Sampling Trees

bioinformatics-1

tools for biolinux

book-pdf-free

books

cafe

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

code-test

cytoscape-tutorials

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

daily_py

save daily code

densitree

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

emblmygff3

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

fxtools

FxTools: a comprehensive toolkit for FASTA and FASTQ file manipulation

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

mpi-bucky

A parallel implementation of BUCKy using OpenMPI message passing interface

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).

plot_demo_code

plotly.py

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

plotmcmcoutput

Shell scripts (bash) for plotting MCMC output (e.g., from MrBayes v.3, BEAST, etc) using gnuplot

poplddecay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

protein-go-term-annotation

pycharm