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phylogenetics

Here are 431 public repositories matching this topic...

biopython / biopython

Official git repository for Biopython (originally converted from CVS)

python bioinformatics genomics protein-structure dna protein biopython phylogenetics sequence-alignment

Updated Dec 4, 2022
Python

etetoolkit / 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.

visualization python phylogenetics tree-structure phylogenomic treeview

Updated Nov 28, 2022
Python

GTDBTk

Ecogenomics / GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

bioinformatics nomenclature taxonomy metagenomics phylogenetics bacteria archaea species-assignments

Updated Dec 1, 2022
Python

amkozlov / raxml-ng

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

bioinformatics mpi phylogenetics pthreads maximum-likelihood

Updated Sep 6, 2022
C++

CompEvol / beast2

Bayesian Evolutionary Analysis by Sampling Trees

java evolution beast phylogenetics bayesian-inference mcmc

Updated Dec 4, 2022
Java

edgardomortiz / vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

snps binary nexus vcf phylogenetics alignment fasta snapp phylip vcf-files polyploid haploid phylogenetic-analysis outgroup convert-snps vcf-format phylip-matrix diploid

Updated Nov 19, 2021
Python

NBISweden / 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:

bioinformatics phylogenetics research-tool bayesian-inference markov-chain-monte-carlo

Updated May 10, 2022
C

veg / hyphy

HyPhy: Hypothesis testing using Phylogenies

science c-plus-plus phylogenetics bioinfomatics

Updated Dec 4, 2022
HyPhy

Cibiv / IQ-TREE

Efficient phylogenomic software by maximum likelihood

phylogenetics model-selection mixture-model maximum-likelihood phylogenomics iq-tree ultrafast-bootstrap

Updated Nov 4, 2021
C++

neherlab / treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Updated Oct 30, 2022
Jupyter Notebook

beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees

java evolution beast phylogenetics mcmc bayesian-analysis

Updated Nov 23, 2022
Java

stephaneguindon / phyml

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

evolution phylogenetics mcmc

Updated Nov 14, 2022
C

tskit

tskit-dev / tskit

Population-scale genomics

python science bioinformatics genomics phylogenetics tree-sequences

Updated Nov 30, 2022
Python

biologyguy / BuddySuite

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

python workflow bioinformatics command-line biology dna protein phylogenetics alignment

Updated Dec 6, 2021
Python

FePhyFoFum / phyx

phylogenetics tools for linux (and other mostly posix compliant) computers

simulation phylogenetics molecular-evolution

Updated Aug 19, 2022
C++

usher

yatisht / usher

Ultrafast Sample Placement on Existing Trees

phylogenetics genome-browser phylogenetic-placement maximum-parsimony usher sars-cov-2

Updated Dec 1, 2022
C++

hahnlab / CAFE

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

bioinformatics phylogenetics gene-families

Updated Apr 7, 2021
C++

kharchenkolab / numbat

Haplotype-aware CNV analysis from scRNA-Seq

phylogenetics cancer-genomics single-cell cnv-detection

Updated Nov 29, 2022
R

ODiogoSilva / TriFusion

Streamlining phylogenomic data gathering, processing and visualization

visualization python gui genetics kivy phylogenetics orthologues phylogenomic

Updated Sep 26, 2018
Python

MicrobeTrace

CDCgov / MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

bioinformatics genomics phylogenetic-trees phylogenetics epidemiology network-visualization hiv cdc phylogenomics phylogeny sequence-alignment genomic-data-analysis genomics-visualization pathogens

Updated Dec 4, 2022
TypeScript

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