jhcepas

TreeProfiler

tree visualization for tree + annotation data

Python

All Algorithms implemented in Python

ngless

NGLess: NGS with less work

diskhash

Diskbased (persistent) hashtable

zxcvbn

Low-Budget Password Strength Estimation

eggnog-clustering

MATAFILER

Metagenomic assembly, genome reconstruction and functional as well as taxonomic profiling

sdm

Fast tool for sequence related tasks

Rarefaction

Rarefaction scripts

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

emapper-benchmark

Raw data and scripts used to benchmark eggnog-mapper. Analysis and additional tests cases are provided as a python notebook.

treematcher

Search flexible patterns within tree structures using regular expression like syntax.

theta

colorization

Automatic colorization using deep neural networks. "Colorful Image Colorization." In ECCV, 2016.

IQ-TREE

Efficient phylogenomic software by maximum likelihood

genbank-browser

a genbank file browser using genome-view and biopython. Use example: http://ct.bork.embl.de/ctbrowser/

cookbook

ext_apps

A compilation of external software used by ETE

MICA

MIcrobiomes using Compressive Acceleration

utils

scripts and utilities related to the Quest for Orthologs intiative

benchmark-webservice

This repository contains the codebase that runs the webservice to benchmark orthology predictions on a common reference proteome dataset.

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

TADbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

vispy

Main repository for Vispy

phyml

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

diamond

Accelerated BLAST compatible local sequence aligner.

scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

somoclu

Massively parallel self-organizing maps: accelerate training on multicore CPUs, GPUs, and clusters

StarCluster

StarCluster is an open source cluster-computing toolkit for Amazon's Elastic Compute Cloud (EC2).