Pinned Repositories
eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
emapper-benchmark
Raw data and scripts used to benchmark eggnog-mapper. Analysis and additional tests cases are provided as a python notebook.
cookbook
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.
treematcher
Search flexible patterns within tree structures using regular expression like syntax.
GDAV
Materials for the Computational Master subject `Genomic Data Analysis and Visualization`
sge-tweaks
My scripts and configs for grid engine
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)
jhcepas's Repositories
jhcepas/GDAV
Materials for the Computational Master subject `Genomic Data Analysis and Visualization`
jhcepas/sge-tweaks
My scripts and configs for grid engine
jhcepas/genbank-browser
a genbank file browser using genome-view and biopython. Use example: http://ct.bork.embl.de/ctbrowser/
jhcepas/npr
Nested Phylogenetic Reconstruction approach (related: https://peerj.com/preprints/223/).
jhcepas/phylogenetic-XML-python-parsers
Python bindings to XML phylogenetic formats (PhyloXML, NeXML, OrthoXML)
jhcepas/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)
jhcepas/decaf_seq_annotation
jhcepas/bcbio-conda
conda recipes for bcbio python code and dependencies
jhcepas/Bio-HMM-Logo
Bio::HMM::Logo - Build logo graphics from HMM files
jhcepas/bioconda-recipes
Conda recipes for the bioconda channel.
jhcepas/bioconda-utils
Utilities for building and managing bioconda recipes
jhcepas/build_portable_npr
Scripts and utils to buil portable package of ETE-NPR
jhcepas/CDE
CDE: Code, Data, and Environment packaging for Linux
jhcepas/crender
python/C tests
jhcepas/discoreg
jhcepas/emacs.d
my personal emacs config
jhcepas/evolwar
jhcepas/fullhouse
a minimal job balancer in python
jhcepas/GSoC
OBF Google Summer of Code
jhcepas/hh-suite
Remote protein homology detection suite.
jhcepas/jhcepas.github.io
personal site
jhcepas/mgv
metagenomic variation tools
jhcepas/numpy
Numpy main repository
jhcepas/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
jhcepas/phylostylotastic
Styled publication of NeXML/NeXSON trees
jhcepas/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"
jhcepas/scikit-bio
Core objects, functions and statistics for working with biological data in Python.
jhcepas/spacemacs
A community-driven Emacs distribution - The best editor is neither Emacs nor Vim, it's Emacs *and* Vim!
jhcepas/stv
jhcepas/tree_formats