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BenoitMorel

BenoitMorel

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BenoitMorel's starred repositories

thirdkind

Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels

Language:RustLicense:NOASSERTIONStargazers:13Issues:0Issues:0

PyPythia

Lightweight python library for predicting the difficulty of alignments in phylogenetics

Language:PythonLicense:GPL-3.0Stargazers:16Issues:0Issues:0

DISCO

Decomposition Into Single-COpy gene trees (DISCO) is a method for decomposing multi-copy gene-family trees while attempting to preserve orthologs and discard paralogs.

Language:PythonStargazers:9Issues:0Issues:0

ASTRID

Fast, accurate species tree estimation.

Language:C++License:GPL-2.0Stargazers:11Issues:0Issues:0

openvpn-build

OpenVPN Build

Language:RoffStargazers:324Issues:0Issues:0

eco-freq

Dynamic CPU/GPU power scaling to maximize renewable energy usage and reduce emissions

Language:PythonLicense:NOASSERTIONStargazers:13Issues:0Issues:0

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:

Language:CLicense:GPL-3.0Stargazers:231Issues:0Issues:0

thesis

My dissertation / PhD thesis

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modeltest

Best-fit model selection

Language:C++License:GPL-3.0Stargazers:73Issues:0Issues:0

phylo-io

Phylo.IO JS tree viewer

Language:JavaScriptLicense:MITStargazers:28Issues:0Issues:0

genesis

A library for working with phylogenetic and population genetic data.

Language:C++License:GPL-3.0Stargazers:56Issues:0Issues:0

QuartetScores

Code for computing various support scores for internodes

Language:C++License:GPL-3.0Stargazers:18Issues:0Issues:0

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.

Language:PythonLicense:GPL-3.0Stargazers:773Issues:0Issues:0

A-pro

ASTRAL for PaRalogs and Orthologs

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SimPhy

SimPhy: A comprehensive simulator of gene family evolution

Language:CLicense:GPL-2.0Stargazers:27Issues:0Issues:0

ALE

Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.

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Seq-Gen

Sequence simulator

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Zombi

Evolution simulator with extinct lineages

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ASTRAL

Accurate Species TRee ALgorithm

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raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible

Language:C++License:AGPL-3.0Stargazers:381Issues:0Issues:0

softwipe

Check and score C/C++ software quality

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python-newick

python package to read and write the Newick format

Language:PythonLicense:Apache-2.0Stargazers:46Issues:0Issues:0

kahypar

KaHyPar (Karlsruhe Hypergraph Partitioning) is a multilevel hypergraph partitioning framework providing direct k-way and recursive bisection based partitioning algorithms that compute solutions of very high quality.

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