146 Open source projects that are alternatives of or similar to phyml

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

Bayesian Evolutionary Analysis Sampling Trees

Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.

Bayesian Evolutionary Analysis by Sampling Trees

A common framework for implementing and using log densities for inference.

Ultrafast Sample Placement on Existing Trees

Blang's software development kit

An R package to manipulate MCMC samples

Pieces of code that have appeared on my blog with a focus on stochastic simulations.

Tracking and proposing changes to SDL's public APIs.

♥ Fast and Accurate Estimation of Evolutionary Distances

machine learning

Examples for Bayesian inference using DynamicHMC.jl and related packages.

A statistical toolbox for diffusion processes and stochastic differential equations. Named after the Brownian Bridge.

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

DynamicHMC versions of StatisticalRethinking models

booster.c3bi.pasteur.fr

Data visualization tool for wikis evolution

Ancestor character reconstruction and visualisation for rooted phylogenetic trees

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

Single-cell copy number calling and event history reconstruction.

Python package and CLI for whole-genome duplication related analyses

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Bayesian Deep Learning with Stochastic Gradient MCMC Methods

Latent Dirichlet Allocation

Evolution Simulation in XNA Refresh

EXONA: The Evolutionary eXploration of Neural Networks Framework -- EXACT, EXALT and EXAMM

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

Bayesian nowcasting with adjustment for delayed and incomplete reporting to estimate COVID-19 infections in the United States

CorBinian: A toolbox for modelling and simulating high-dimensional binary and count-data with correlations

A web interface for exploring PyMC3 traces

Application of the L2HMC algorithm to simulations in lattice QCD.

Equilibrium Expectation for ERGM parameter estimation for large directed networks

Biological Sequence Substitution Models for Julia

De novo annotation of young retrotransposons

Visualize the evolution of a file tracked by git

The sample question for Interview a job in Binary options

Supported highly optimized and flexible genetic algorithm package for python

Sequential Tree Sampler for online phylogenetics

Alignment editor for Mac OS X

A Python package for gene-centric taxonomic and functional classification using phylogenetic placement

Multi-core BUGS for fast Bayesian inference of large hierarchical models

Pinpoints the mutation favored by selection

BAS R package https://merliseclyde.github.io/BAS/

Using neural network to build expressive hierarchical distribution; A variational method to accurately estimate posterior uncertainty; A fast and general method for Bayesian inference. (ICML 2018)

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

A tool for exploring very large trees in the browser

Material for a workshop on Bayesian stats with R

Configuration tutorials for a variety of mail user agents.

Regression with Summary Statistics.

Citylines.co is a collaborative platform for mapping the transit systems of the world!

A Framework for Coalescent Simulation in R

Nested Sampling post-processing and plotting

Evolution simulator

Helping humanity evolve

Bayesian Generalized Linear Models with Time-Varying Coefficients

Write DB migrations with SQL and run them with a CLI

A C++ library of Markov Chain Monte Carlo (MCMC) methods