37 Open source projects that are alternatives of or similar to sts

Sequential Monte Carlo algorithm for approximation of posterior distributions.

♥ Fast and Accurate Estimation of Evolutionary Distances

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

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

A tool for exploring very large trees in the browser

pyABC: distributed, likelihood-free inference

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

Official git repository for Biopython (originally converted from CVS)

Phylogenetic Likelihood Library

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

Phylogenetic trees in Julia

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

Version 5 of the CAFE phylogenetics software

A library for working with phylogenetic and population genetic data.

Python version of PHLAWD

A course in the theory and practice of phylogenetic inference from DNA sequence data

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

Alignment editor for Mac OS X

Ancestor character reconstruction and visualisation for rooted phylogenetic trees

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

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

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).

Implementing semantically rich NeXML I/O in R

Biological Sequence Substitution Models for Julia

booster.c3bi.pasteur.fr

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

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

Ultrafast Sample Placement on Existing Trees

⚡ Lightning fast density estimation in Julia ⚡

R package for online training of regression models using FTRL Proximal

ML algorithm for real-time classification

Streaming, Memory-Limited, r-truncated SVD Revisited!

If you can measure it, consider it predicted

Particle filtering and sequential parameter inference in Python

A probabilistic programming language that combines automatic differentiation, automatic marginalization, and automatic conditioning within Monte Carlo methods.

R package for statistical inference using partially observed Markov processes

Collected code and materials from the intensive course preparing for the workshop on Sequential Monte Carlo (SMC) methods at Uppsala University, August 2017