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Awesome

An open API service indexing awesome lists of open source software.

Projects in Awesome Lists tagged with phylogenetic-trees

A curated list of projects in awesome lists tagged with phylogenetic-trees .

https://github.com/YuLab-SMU/ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees

annotations ggplot2 phylogenetic-trees r visualization

Last synced: 06 May 2025

https://github.com/biobakery/phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

biobakery phylogenetic-trees python tools

Last synced: 16 May 2025

https://github.com/biobakery/graphlan

High-quality circular representations of taxonomic and phylogenetic trees

biobakery circular-visualization phylogenetic-trees python taxonomic-trees tools

Last synced: 10 Apr 2025

https://github.com/lkremer/cafe_fig

A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)

cafe ete3 evolution gene-families molecular-evolution phylogenetic-trees

Last synced: 09 May 2025

https://github.com/moshi4/phytreeviz

Simple phylogenetic tree visualization python package for phylogenetic analysis

bioinformatics biopython matplotlib phylogenetic-trees python visualization

Last synced: 17 Mar 2025

https://github.com/daijiang/rtrees

rtrees: an R package to assemble phylogenetic trees from mega-trees

phylogenetic-trees r r-package rstats

Last synced: 07 May 2025

https://github.com/ms609/treedist

Calculate distances between phylogenetic trees in R

phylogenetic-trees r r-package rstats tree-distances trees

Last synced: 09 Apr 2025

https://github.com/albertyw/itolapi

Python API for the Interactive Tree of Life (iTOL)

bioinformatics computational-biology phylogenetic-trees phylogenetics python visualization

Last synced: 16 Mar 2025

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: 09 May 2025

https://github.com/ms609/treetools

Create, modify and analyse phylogenetic trees in R

cran evolutionary-biology phylogenetic-trees phylogenetics r-package

Last synced: 08 May 2025

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: 21 Apr 2025

https://github.com/dombennett/treeman

:deciduous_tree::man: An R package for manipulating phylogentic trees

bioinformatics cran evolution phylogenetic-trees

Last synced: 13 Jan 2025

https://github.com/ms609/quartet

R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)

bioinformatics comparison cran phylogenetic-trees phylogenetics quartet quartet-distance research-tool tree

Last synced: 13 Jan 2025

https://github.com/klausvigo/shinytreeviewer

A simple treeviewer based on the R packages ape and phangorn.

phylogenetic-trees r shiny

Last synced: 07 Apr 2025

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: 15 Apr 2025

https://github.com/thijsjanzen/nltt

Repository for the R nLTT package

nltt nltt-statistic package phylogenetic-trees phylogenetics r

Last synced: 17 Mar 2025

https://github.com/davised/automlsa2

Automated Multi-Locus Sequence Analysis phylogenetic tree construction software

bioinformatics phylogenetic-trees python3

Last synced: 09 Apr 2025

https://github.com/uscbiostats/jsphylosvg

htmlwidgets for the jsPhyloSVG javascript library

htmlwidgets phylogenetic-trees phylogenetics r rpackage rstats

Last synced: 28 Apr 2025

https://github.com/pierrebarbera/scrapp

Species Counting on Reference trees viA Phylogenetic Placements

phylogenetic-diversity phylogenetic-trees phylogenetics

Last synced: 13 Apr 2025

https://github.com/linsalrob/phageproteomictree

The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance

awesomeness bioinformatics evolution evolutionary-algorithms phage phylogenetic-trees phylogenetics taxonomy

Last synced: 23 Mar 2025

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

Phylogenetic simulation and inference in Julia

julia nucleotide-substitution-models phylogenetic-trees

Last synced: 12 Feb 2025

https://github.com/d-dawg78/comp561-final-project

McGill University - Computational Biology Methods and Research Project

gene-evolution maximum-parsimony needleman-wunsch phylogenetic-trees sequence-alignment

Last synced: 04 Apr 2025

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: 12 Apr 2025

https://github.com/dustinmichels/pl-phylogeny

Evolutionary trees of programming languages, derived from analagous code snippets.

bioinformatics evolution phylogenetic-trees programming-languages python

Last synced: 07 Apr 2025

https://github.com/robaina/jplaceparser

A python parser for jplace (evolutionary placement) files

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

Last synced: 08 Apr 2025

https://github.com/ms609/rogue

Identify rogue taxa in phylogenetic trees within R

consensus-tree phylogenetic-trees phylogenetics r-package

Last synced: 02 Mar 2025

https://github.com/saptak625/cladogramgeneratoralgorithm

Cladogram Generation Algorithm made using Python

cladogram evolution phylogenetic-trees python trees treetraversal

Last synced: 21 Mar 2025

https://github.com/noedemange/labelcolor

App Shiny : Scalable visualization of groups within a hierarchical clustering from binary data matrix.

color label phylogenetic-trees phylogeny r rstats shiny

Last synced: 27 Feb 2025

https://github.com/uscbiostats/pruner

pruner: Implementing the Felsenstein's Tree Pruning algorithm

cpp cpp11 header-only phylogenetic-trees phylogenetics pruning tree

Last synced: 26 Feb 2025

https://github.com/walterxie/startingtree

nice algorithm to initialize starting trees in BEAST2

beast2 phylogenetic-trees temporal

Last synced: 28 Mar 2025

https://github.com/ms609/tbrdist

An R package to calculate tree rearrangement distances

distance-calculation phylogenetic-trees phylogenetics r

Last synced: 02 Mar 2025

https://github.com/tripal/tripal_dt

An example module released during PAG 2017 hackathon, that displays a D3JS tree from the phylonode table.

d3js phylogenetic-trees tripal visualization

Last synced: 09 Apr 2025

https://github.com/muntashirakon/phpphylogenetictrees

A simple PHP library to build phylogenic trees from distance matrix

distance-matrix nj php-library phylogenetic-trees upgma

Last synced: 24 Mar 2025

https://github.com/simongreenhill/pylento

PyLento -- a python tool for calculating splits from phylogenetic data and plotting Lento plots.

phylogenetic-trees phylogenetics

Last synced: 20 Mar 2025