Projects in Awesome Lists tagged with phylogenetics

https://github.com/biopython/biopython

Official git repository for Biopython (originally converted from CVS)

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

Last synced: 16 Dec 2024

https://github.com/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.

phylogenetics phylogenomic python tree-structure treeview visualization

Last synced: 15 Nov 2024

https://github.com/neherlab/treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

phylogenetics

Last synced: 18 Dec 2024

https://github.com/klausvigo/phangorn

Phylogenetic analysis in R

phylogenetic-analysis phylogenetics r

Last synced: 20 Dec 2024

https://github.com/theosanderson/taxonium

A tool for exploring large trees in the browser

deckgl phylogenetics phylogeny react tree virus

Last synced: 16 Dec 2024

https://github.com/evogytis/baltic

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).

phylogenetics visualisation

Last synced: 15 Nov 2024

https://github.com/odiogosilva/trifusion

Streamlining phylogenomic data gathering, processing and visualization

genetics gui kivy orthologues phylogenetics phylogenomic python visualization

Last synced: 20 Dec 2024

https://github.com/zsailer/phylopandas

Pandas DataFrames for phylogenetics

biopython pandas phylogenetics python

Last synced: 27 Oct 2024

https://github.com/moshi4/aniclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes

bioinformatics comparative-genomics genomics microbial-genomics phylogenetics phylogenomics python taxonomy visualization

Last synced: 22 Dec 2024

https://github.com/pierrebarbera/epa-ng

Massively parallel phylogenetic placement of genetic sequences

bioinformatics mpi mpi-io openmp phylogenetics placement taxonomic-classification

Last synced: 31 Oct 2024

https://github.com/jlsteenwyk/clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

bioinformatics evolution evolutionary-biology genomics phylogenetics phylogenomics python systematics

Last synced: 21 Dec 2024

https://github.com/JLSteenwyk/ClipKIT

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

bioinformatics evolution evolutionary-biology genomics phylogenetics phylogenomics python systematics

Last synced: 18 Nov 2024

https://github.com/jlsteenwyk/phykit

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

bioinformatics evolution evolutionary-biology genomics multiple-sequence-alignments phylogenetics phylogenomics python

Last synced: 21 Dec 2024

https://github.com/lczech/genesis

A library for working with phylogenetic and population genetic data.

c-plus-plus evolutionary-placement phylogenetic-data phylogenetic-placements phylogenetic-trees phylogenetics placement pool-sequencing population-genetics

Last synced: 17 Dec 2024

https://github.com/lczech/gappa

A toolkit for analyzing and visualizing phylogenetic (placement) data

c-plus-plus evolutionary-placement gappa genesis phylogenetic-data phylogenetic-placement phylogenetics placement

Last synced: 18 Dec 2024

https://github.com/lh3/jstreeview

Interactive phylogenetic tree viewer/editor

bioinformatics phylogenetics

Last synced: 17 Nov 2024

https://github.com/nextstrain/mpox

Nextstrain build for mpox virus

augur auspice bioinformatics genbank genomic-epidemiology metadata monkeypox mpox nextstrain pathogen phylogenetics pipeline virus-evolution

Last synced: 18 Dec 2024

https://github.com/ropensci/babette

babette is an R package to work with BEAST2

bayesian-inference beast2 phylogenetics r r-package rstats

Last synced: 04 Dec 2024

https://github.com/ecojulia/phylo.jl

Simple phylogenetic trees in Julia to work with Diversity.jl - https://github.com/EcoJulia/Diversity.jl

julia phylogenetics

Last synced: 18 Dec 2024

https://github.com/albertyw/itolapi

Python API for the Interactive Tree of Life (iTOL)

bioinformatics computational-biology phylogenetic-trees phylogenetics python visualization

Last synced: 27 Oct 2024

https://github.com/jamiemcg/busco_phylogenomics

BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins

bayesian bioinformatics evolution genomics maximum-likelihood phylogenetics phylogenomics

Last synced: 20 Nov 2024

https://github.com/datasnakes/orthoevolution

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

bash bioinformatics biology biosql blast data-science ftp genetics ncbi orthologs orthologues orthology orthology-inference pbs phylogenetics python qsub sequence-alignment sge shell

Last synced: 16 Nov 2024

https://github.com/lkremer/showtree

showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.

ete3 gene-families phylogenetic-trees phylogenetics protein-domains protein-families python treeview visualization

Last synced: 18 Nov 2024

https://github.com/jlsteenwyk/orthofisher

a broadly applicable tool for automated gene identification and retrieval

bioinformatics evolution evolutionary-biology genomics orthology orthology-assignments orthology-inference phylogenetics phylogenomics python

Last synced: 19 Dec 2024

https://github.com/4ment/seqotron

Alignment editor for Mac OS X

macosx phylogenetics sequence-viewer tree-viewer

Last synced: 07 Nov 2024

https://github.com/theosanderson/chronumental

Estimating time trees from very large phylogenies

jax numpyro phylogenetics timetree

Last synced: 18 Nov 2024

https://github.com/biocore/q2-qemistree

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

cheminformatics fragmentation-trees metabolomics microbiome phylogenetics

Last synced: 18 Nov 2024

https://github.com/4ment/phylostan

Phylogenetic inference using Stan

bayes hmc phylogenetics pystan stan variational-inference

Last synced: 07 Nov 2024

https://github.com/jangevaare/phylotrees.jl

Phylogenetic trees in Julia

bioinformatics julia phylogenetic-trees phylogenetics

Last synced: 08 Nov 2024

https://github.com/moshi4/cafeplotter

A tool for plotting CAFE5 gene family expansion/contraction result

bioinformatics evolution matplotlib molecular-evolution phylogenetic-trees phylogenetics phylogenomics python

Last synced: 09 Nov 2024

https://github.com/jlsteenwyk/orthosnap

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

bioinformatics evolution evolutionary-biology genomics orthology orthology-assignments orthology-inference phylogenetics phylogenomics python

Last synced: 08 Nov 2024

https://github.com/fmichonneau/phylobase

An R package that provides a base S4 class for comparative methods, incorporating one or more trees and trait data

phylogenetics r

Last synced: 14 Oct 2024

https://github.com/biojulia/substitutionmodels.jl

Biological Sequence Substitution Models for Julia

bioinformatics julia phylogenetics substitution-models

Last synced: 08 Nov 2024

https://github.com/rvosa/bio-phylo

Bio::Phylo - Phyloinformatic analysis using Perl

bioinformatics computational-biology evolution perl phylogenetics toolkit

Last synced: 27 Oct 2024

https://github.com/4ment/physher

A multi-algorithmic framework for phylogenetic inference

bayesian-inference c genetic-algorithm maximum-likelihood mcmc phylogenetics variational-inference

Last synced: 07 Nov 2024

https://github.com/daviddao/exelixis

Interactive and easy-to-use phylogenetic tree viewer for the web

biojs javascript phylogenetics visualisation

Last synced: 14 Oct 2024

https://github.com/lkremer/msa_trimmer

Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.

aligned-regions alignment-trimming cds-alignment codeml codon-alignment molecular-evolution msa-trimmer multiple-sequence-alignment paml phylogenetics sequence-alignment trimmer trimming

Last synced: 18 Nov 2024

https://github.com/hhandika/segul

An ultrafast and memory efficient tool for phylogenomics

alignment bioinformatics command-line-tool phylogenetics phylogenomics rust

Last synced: 17 Nov 2024

https://github.com/ropensci/rnexml

Implementing semantically rich NeXML I/O in R

nexml phylogenetics r r-package rstats

Last synced: 16 Dec 2024

https://github.com/4ment/torchtree

A probabilistic framework in PyTorch for phylogenetic models

phylogenetics pytorch variational-inference

Last synced: 07 Nov 2024

https://github.com/tguillerme/multree

Performs MCMCglmm on multiple phylogenetic trees

bayesian comparative-genomics mcmcglmm multiple-trees phylogenetics r

Last synced: 13 Nov 2024

https://github.com/hopkinsidd/phylosamp

The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linkage and sample size calculations for phylogenetic studies.

package phylogenetics r sampling

Last synced: 08 Nov 2024

https://github.com/zsailer/phylovega

Interactive tree visualizations in Python (powered by Vega).

pandas phylogenetics python vega

Last synced: 27 Oct 2024

https://github.com/ax3man/phylopath

Perform phylogenetic path analysis in R.

analysis comparative-methods path phylogenetics r rstats

Last synced: 20 Nov 2024

https://github.com/aaboyles/microbetrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

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

Last synced: 08 Nov 2024

https://github.com/zsailer/pyasr

Ancestral Sequence Reconstruction in Python

evolution pandas phylogenetics python

Last synced: 27 Oct 2024

https://github.com/AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

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

Last synced: 07 Nov 2024

https://github.com/colelyman/kleuren

Find bubbles in the Colored de Bruijn Graph to reconstruct phylogenetic trees

bioinformatics de-bruijn-graphs phylogenetics phylogeny

Last synced: 07 Nov 2024

https://github.com/evoinfo/miapa

Minimum Information About a Phylogenetic Analysis (MIAPA) vocabularies and tools

information-exchange minimum-information obofoundry phylogenetics standard

Last synced: 23 Oct 2024

https://github.com/dschrempf/elynx

Analyze, modify and simulate molecular sequence data and phylogenetic trees in a reproducible way.

bioinformatics haskell phylogenetics

Last synced: 12 Oct 2024

https://github.com/cran-task-views/phylogenetics

CRAN Task View: Phylogenetics

cran phylogenetics r rstats task-views

Last synced: 27 Nov 2024

https://github.com/armanbilge/phylohmc

Hamiltonian Monte Carlo on the space of phylogenies

bayesian-inference hamiltonian-monte-carlo phylogenetics statistics

Last synced: 17 Oct 2024

https://github.com/nextstrain/ncov-clades-schema

Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain

clades nextstrain phylogenetics sars-cov-2

Last synced: 18 Dec 2024

https://github.com/biojulia/phylogenies.jl

The BioJulia package for working with phylogenetic trees and geneologies.

bioinformatics biology evolution phylogenetic-trees phylogenetics phylogenomics

Last synced: 08 Dec 2024

https://github.com/fmichonneau/rncl

An R interface to the Nexus Class Library (C++) to read in quickly large phylogenetic trees and data

newick nexus phylogenetics r tree-parsing

Last synced: 14 Oct 2024

https://github.com/simongreenhill/treemaker

A Python library for creating a Newick formatted tree from a set of classification strings

classification newick newick-format phylogenetics python taxonomy

Last synced: 26 Nov 2024

https://github.com/sysbiochalmers/hgtphylodetect

HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.

evolutionary-biology high-throughput-pipeline horizontal-gene-transfer phylogenetics sequence-analysis systems-biology

Last synced: 03 Dec 2024

https://github.com/uscbiostats/aphylo

Statistical inference of genetic functions in phylogenetic trees

annotations inference phylogenetics r r-package rcpparmadillo

Last synced: 10 Oct 2024

https://github.com/joshwlambert/daisieprep

Extracts phylogenetic island community data from phylogenetic trees

data-science island-biogeography phylogenetics r

Last synced: 27 Oct 2024

https://github.com/thijsjanzen/nltt

Repository for the R nLTT package

nltt nltt-statistic package phylogenetic-trees phylogenetics r

Last synced: 27 Oct 2024

https://github.com/pierrebarbera/scrapp

Species Counting on Reference trees viA Phylogenetic Placements

phylogenetic-diversity phylogenetic-trees phylogenetics

Last synced: 31 Oct 2024

https://github.com/smithsonian/fabaceae_phylogenomics_workflow

Target-enrichment data processing in legumes

legumes molecular-evolution phylogenetics target-enrichment

Last synced: 08 Nov 2024

https://github.com/uscbiostats/jsphylosvg

htmlwidgets for the jsPhyloSVG javascript library

htmlwidgets phylogenetic-trees phylogenetics r rpackage rstats

Last synced: 11 Nov 2024

https://github.com/gvegayon/phylo-software

List of phylogenetic software. Original from Prof. Felsenstein's website https://evolution.gs.washington.edu/phylip/software.html

archive felsenstein genetics phylogenetics software

Last synced: 22 Dec 2024

https://github.com/lczech/thesis

My dissertation / PhD thesis

phylogenetic-placement phylogenetics thesis

Last synced: 01 Dec 2024

https://github.com/4ment/marginal-experiments

19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology

data data-visualization marginal-likelihood phylogenetics

Last synced: 07 Nov 2024

https://github.com/neherlab/nextclade_data_workflows

nextclade nextstrain phylogenetics snakemake virus-evolution

Last synced: 05 Nov 2024

https://github.com/simongreenhill/phylogemetric

Python library for calculating the delta score (Holland et al. 2002) and Q-Residual (Gray et al. 2010)

phylogenetics

Last synced: 26 Nov 2024

https://github.com/biosustain/neighbor-joining

Rapid Neighbor-Joining phylogenetic tree creation method implementation for Node.js

neighbor-joining nodejs phylogenetic-trees phylogenetics

Last synced: 15 Nov 2024

https://github.com/thibaultlatrille/adaptapop

Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale

phylogenetics polymorphic-variants population-genetics scientific-publication

Last synced: 11 Dec 2024

https://github.com/shuyib/phylogenetic-tree-study

Estimating Phylogenetic trees using six microorganisms 16S rRNA gene with Unsupervised Learning, web based tools and Molecular Evolutionary Genetics Analysis MEGA7

16s-rrna bokehplots hierarchical-clustering jupyter-notebook kenya machine-learning microorganism motif-analysis motif-discovery numpy-arrays pandas phylogenetics python scipy unsupervised-learning

Last synced: 28 Nov 2024

https://github.com/audy/tree-of-life

:deciduous_tree: API for NCBI taxonomic lineages

bioinformatics phylogenetics

Last synced: 21 Oct 2024

https://github.com/4ment/phylojax

jax phylogenetics variational-inference

Last synced: 07 Nov 2024

https://github.com/robaina/jplaceparser

A python parser for jplace (evolutionary placement) files

bioinformatics computational-biology evolutionary-algorithms phylogenetic-trees phylogenetics python

Last synced: 22 Dec 2024

https://github.com/dfornika/tree-with-metadata

Draw a phylogenetic tree, along with a table of metadata

metadata phylogenetic-tree phylogenetics visualization

Last synced: 25 Nov 2024

https://github.com/4ment/torchtree-bito

beagle bito phylogenetics pybind11 python torchtree

Last synced: 07 Nov 2024

https://github.com/4ment/flc

Local clock model using relaxed and strict clocks

bayesian beast2 mcmc phylogenetics

Last synced: 07 Nov 2024

https://github.com/neherlab/spike-only

Spike-only SARS-CoV-2 Nextstrain build

augur bioinformatics nextstrain nextstrain-ncov phylogenetics sars-cov-2 sars-cov-2-variants

Last synced: 05 Nov 2024

https://github.com/neherlab/ba286

BA.2.86 project with Sigal lab

bioinformatics computational-biology genomic-epidemiology nextstrain phylogenetics sars-cov-2 sars-cov-2-variants snakemake treetime virus-evolution

Last synced: 05 Nov 2024

https://github.com/zsailer/scipy-2018

"Resurrecting ancient proteins in Python" (SciPy 2018 talk by Zach Sailer)

biopython dendropy pandas phylogenetics scipy2018 vega

Last synced: 22 Dec 2024

https://github.com/joethorley/radcon

A phylogenetic tree consensus and comparison program for Mac OS 9.

consensus phylogenetics radcon supertrees

Last synced: 22 Nov 2024

https://github.com/fomightez/simulated_data

A repository for code that generates various simulated data.

evolutionary expression gene phylogenetics phylogenomics python r rna-seq-analysis rna-seq-data simulated-data

Last synced: 07 Nov 2024

https://github.com/anjasfedo/tree-clustering-problem

Tree Clustering Problem: Clustering Phylogenetic Trees.

clustering machine-learning phylogenetics

Last synced: 16 Nov 2024

https://github.com/uscbiostats/pruner

pruner: Implementing the Felsenstein's Tree Pruning algorithm

cpp cpp11 header-only phylogenetic-trees phylogenetics pruning tree

Last synced: 11 Nov 2024

https://github.com/simongreenhill/ratecounter

Phylogenetic Rate Counter

cultural-phylogeny language-phylogeny phylogenetics

Last synced: 26 Nov 2024

https://github.com/astrabert/altrevis

An easy-to-use, beginner-oriented tool to align DNA/RNA or protein sequences, infer an approximately Maximum Likelihood phylogenetic tree from the alignment and visualize it

alignement beginner-friendly bioinformatics phylogenetics

Last synced: 15 Nov 2024

https://github.com/benmarwick/bayesinfmatcultphylo

Research compendium for our paper "Bayesian inference of material culture phylogenies using continuous traits from the archaeological record: A birth–death model for Late Neolithic/Early Bronze Age arrowheads from Northwestern Europe"

archaeology phylogenetics research-compendium

Last synced: 16 Nov 2024