jhcepas

GDAV

Materials for the Computational Master subject `Genomic Data Analysis and Visualization`

sge-tweaks

My scripts and configs for grid engine

genbank-browser

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

npr

Nested Phylogenetic Reconstruction approach (related: https://peerj.com/preprints/223/).

phylogenetic-XML-python-parsers

Python bindings to XML phylogenetic formats (PhyloXML, NeXML, OrthoXML)

test_branch_support_after_tree_rerooting

Additional test cases of branch support rearrangements after tree re-rooting inspired by http://biorxiv.org/content/early/2015/12/25/035360 (APE, dendropy, biopython, ete3, newick-utilities, bioperl)

decaf_seq_annotation

bcbio-conda

conda recipes for bcbio python code and dependencies

Bio-HMM-Logo

Bio::HMM::Logo - Build logo graphics from HMM files

bioconda-recipes

Conda recipes for the bioconda channel.

bioconda-utils

Utilities for building and managing bioconda recipes

build_portable_npr

Scripts and utils to buil portable package of ETE-NPR

CDE

CDE: Code, Data, and Environment packaging for Linux

crender

python/C tests

discoreg

emacs.d

my personal emacs config

evolwar

fullhouse

a minimal job balancer in python

GSoC

OBF Google Summer of Code

hh-suite

Remote protein homology detection suite.

jhcepas.github.io

personal site

mgv

metagenomic variation tools

numpy

Numpy main repository

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

phylostylotastic

Styled publication of NeXML/NeXSON trees

prx5_supplementary_data

Supplementary material for the paper "Prokaryotic ancestry of a dual localized peroxiredoxin 5 in malaria parasites. Carine F. Djuika, Jaime Huerta-Cepas, Jude M. Przyborski, Sophia Deil, Cecilia P. Sanchez, Tobias Doerks, Peer Bork, Michael Lanzer, Marcel Deponte.Microbial Cell, Vol. 2, No. 1, pp. 5 - 13; DOI: 10.15698/mic2015.01.182"

scikit-bio

Core objects, functions and statistics for working with biological data in Python.

spacemacs

A community-driven Emacs distribution - The best editor is neither Emacs nor Vim, it's Emacs *and* Vim!

stv

tree_formats