Explore @DessimozLab Open Source projects

Dessimoz Lab (@DessimozLab)

DessimozLab

Stars
411
Global Org. Rank 26,868 (Top 9 %)
Registered about 9 years ago
Most used languages

Python
42.9 %

Jupyter Notebook
28.6 %

JavaScript
7.1 %

C
3.6 %

Nextflow 3.6 %

Shell
3.6 %

TeX
3.6 %

HTML
3.6 %

C++
3.6 %

read2tree

a tool for inferring species tree from sequencing reads

fold_tree

snakemake pipeline for creating trees from sequence sets

Jupyter Notebook

OMArk

phylo-io

Phylo.IO JS tree viewer

FastOMA

FastOMA is a scalable software package to infer orthology relationship.

omamer

OMAmer - tree-driven and alignment-free protein assignment to sub-families

matreex

HogProf

Phylogenetic profiling with orthology data

Jupyter Notebook

pyham

pyopa

A fast implementation of optimal pairwise alignments with python

iHam

Widget to visualise the evolutionary history of gene families

pylabeledrf

A package to compute the Robinson Fould distance extended to labeled topologies.

Jupyter Notebook

omamo

OMAMO: orthology-based model organism selection

edgehog

Infering ancestral synteny with hierarchical orthologous groups

ALF

ALF artificial life simulator

go-handbook

Electronic exercises (with solutions) to accompany the book chapter "A Gene Ontology Tutorial in Python" by Alex Warwick Vesztrocy and Christophe Dessimoz, in the collection The Gene Ontology Handbook, C Dessimoz and N Skunca Eds, Spring Humana.

Jupyter Notebook

esprit2

SIBBiodiversityBioinformatics2023

familyanalyzer-deprecated

pyomadb

PyOMADB is a python client to the OMA browser, using the REST API.

OmaStandalone

OMA standalone repository

OmaDB

Jupyter Notebook

treeCl

Phylogenetic clustering package

Archaeal-Fusexins

Discovery of archaeal Fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins

Jupyter Notebook

f1000_OmaPrimer

A complementary analysis to "Identifying Orthologs with OMA: A Primer" in which we show how to compare sub-types of orthologs (pairwise vs. HOG vs. OMA Group)

Jupyter Notebook

blogpost-code

This repo contains code and notebook associated with various blog posts

Jupyter Notebook

f1000_PhylogeneticTree

A tutorial on using OMA Browser and OMA Standalone for phylogenetic species trees reconstruction. Scripts referred to in the tutorial paper can be found here.

nf-oma-browser-build

Nextflow pipeline to convert OMA to OMA browser

pyoma

Python library to interact with OMA hdf5 files