tahiri-lab/aPhyloGeo

aPhyloGeo is a multiplatform application for the analysis of genetic and climatic conditions.

Language: Shell - Size: 66.5 MB - Last synced: 8 days ago - Pushed: about 1 month ago - Stars: 9 - Forks: 4

cmzmasek/forester

forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research

Language: Java - Size: 126 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 33 - Forks: 15

veg/hyphy

HyPhy: Hypothesis testing using Phylogenies

Language: HyPhy - Size: 56.8 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 194 - Forks: 68

KlausVigo/phangorn

Phylogenetic analysis in R

Language: R - Size: 125 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 197 - Forks: 38

biopython/biopython

Official git repository for Biopython (originally converted from CVS)

Language: Python - Size: 67.5 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 4,170 - Forks: 1,713

4ment/torchtree-experiments

Language: R - Size: 138 KB - Last synced: about 9 hours ago - Pushed: about 19 hours ago - Stars: 0 - Forks: 0

cogent3/cogent3

Comparative Genomics Toolkit 3

Language: Python - Size: 41.5 MB - Last synced: about 21 hours ago - Pushed: about 24 hours ago - Stars: 93 - Forks: 52

lepitaxa/lepitaxa.github.io

LEPITAXA – Lepidopteran Classification Project

Language: HTML - Size: 5.34 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 1 - Forks: 0

yatisht/usher

Ultrafast Sample Placement on Existing Trees

Language: C++ - Size: 39.1 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 117 - Forks: 40

amkozlov/raxml-ng

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

Language: C++ - Size: 1.05 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 358 - Forks: 61

nextstrain/mpox

Nextstrain build for mpox virus

Language: Python - Size: 32.4 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 39 - Forks: 16

husonlab/splitstree6

SplitsTree App

Language: Java - Size: 205 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 15 - Forks: 3

tskit-dev/tskit

Population-scale genomics

Language: Python - Size: 17.4 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 142 - Forks: 68

reslp/dockerfiles

A collection of Dockerfiles for different containers I use.

Language: Dockerfile - Size: 321 KB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 2 - Forks: 1

rmcar17/SpectralClusterSupertree

A supertree method for rooted source trees

Language: Python - Size: 45.8 MB - Last synced: about 13 hours ago - Pushed: 2 days ago - Stars: 5 - Forks: 0

Zsailer/scipy-2018

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

Language: Jupyter Notebook - Size: 23.6 MB - Last synced: 2 days ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 2

JLSteenwyk/PhyKIT

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

Language: Python - Size: 17.4 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 47 - Forks: 6

JLSteenwyk/ClipKIT

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Language: Python - Size: 25.7 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 52 - Forks: 4

infinity-a11y/PhyloTrace

PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.

Language: R - Size: 18.1 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 3 - Forks: 0

CDCgov/MicrobeTrace Fork of AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Language: TypeScript - Size: 124 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 83 - Forks: 37

stephaneguindon/phyml

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

Language: C - Size: 26.6 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 166 - Forks: 60

ch1ru/genome-lab

A bioinformatics web app for comparative genomics

Language: TypeScript - Size: 201 KB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

AndreaRubbi/Pear-EBI

Calculates distances of trees in large collections. Embeds distances and plot the embeddings with dynamic interfaces.

Language: HTML - Size: 358 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 2 - Forks: 2

coldham10/SCarborSNV

SCarborSNV is an efficient algorithm for phylogeny aware genotyping of single cell genomes, using dynamic programming and neighbor joining.

Language: C - Size: 25.3 MB - Last synced: 4 days ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

biocaml/phylogenetics

Algorithms and datastructures for phylogenetics

Language: OCaml - Size: 604 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 12 - Forks: 0

hhandika/segul

An ultrafast and memory efficient tool for phylogenomics

Language: Rust - Size: 1.54 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 13 - Forks: 0

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

Language: Jupyter Notebook - Size: 3.45 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 3 - Forks: 5

sishuowang/Solutions_Manual_CME2006_MESA2014

A solutions manual for all excercises in the Ziheng Yang's two seminall books on statistical molecular evolution: Computational Molecular Evolution (Yang 2006) and Molecular Evolution: A Statistical Approach (Yang 2014).

Language: Perl - Size: 89.3 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 7 - Forks: 1

evolbioinfo/pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

Language: Python - Size: 36.2 MB - Last synced: 3 days ago - Pushed: 2 months ago - Stars: 25 - Forks: 5

computations/root_digger

A tool to root phylogenies

Language: C++ - Size: 8.8 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 20 - Forks: 7

phylotastic/datelife

R package containing datelife's core functionality

Language: R - Size: 237 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 11 - Forks: 11

Wytamma/beastiary

Real time and remote MCMC trace monitoring with BEASTIARY.

Language: Vue - Size: 54.2 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 16 - Forks: 2

EcoJulia/Phylo.jl

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

Language: Julia - Size: 14.7 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 32 - Forks: 13

drboothtj/getphylo

a python package for automated generation of phylogenetic trees from genbank files

Language: Python - Size: 75.8 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 13 - Forks: 0

jjmccollum/teiphy

A Python package for converting TEI XML collations to NEXUS and other formats

Language: Python - Size: 9.01 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 9 - Forks: 2

PierreBarrat/TreeTools.jl

Tools for handling phylogenetic or genealogic trees with Julia. Mainly serves as a dependency for my other package TreeKnit

Language: Julia - Size: 771 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 5 - Forks: 1

Ecogenomics/GTDBTk

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

Language: Python - Size: 28.7 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 430 - Forks: 83

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.

Language: Python - Size: 125 MB - Last synced: 7 days ago - Pushed: 27 days ago - Stars: 752 - Forks: 215

AndrewQuijano/Treespace_REU_2017

Python code to compute metrics on Rooted Phylogenetic Networks

Language: Python - Size: 479 KB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 3 - Forks: 0

raw-lab/NFixDB

Comprehensive database for diazotroph nitrogenases, alternative nitrogenases, and nitrogenase-like enzymes at the University of North Carolina at Charlotte (UNCC)

Language: Python - Size: 218 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 4 - Forks: 1

nextstrain/ncov-clades-schema

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

Language: JavaScript - Size: 434 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 9 - Forks: 7

theosanderson/taxonium

A tool for exploring very large trees in the browser

Language: JavaScript - Size: 251 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 90 - Forks: 16

dschrempf/elynx

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

Language: Haskell - Size: 76.8 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 9 - Forks: 0

jbloomlab/phydms

phylogenetic analyses informed by deep mutational scanning data

Language: HTML - Size: 15.4 MB - Last synced: 11 days ago - Pushed: about 3 years ago - Stars: 14 - Forks: 3

moshi4/CafePlotter

A tool for plotting CAFE5 gene family expansion/contraction result

Language: Python - Size: 3.77 MB - Last synced: 6 days ago - Pushed: 7 months ago - Stars: 19 - Forks: 3

fomightez/simulated_data

A repository for code that generates various simulated data.

Language: Python - Size: 1000 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 1 - Forks: 0

BCCDC-PHL/civet Fork of artic-network/civet

Cluster Investigation & Virus Epidemiology Tool

Size: 43.2 MB - Last synced: 12 days ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

ms609/Quartet

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

Language: C++ - Size: 12.8 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 8 - Forks: 5

RhettRautsaw/PhyProbe

PhyProbe is a bioinformatic pipeline designed to extract phylogenetic loci from Next-Generation Sequencing datasets including RNAseq, WGS, and Sequence/Target Capture methodologies (e.g., AHE, UCEs).

Language: Python - Size: 890 KB - Last synced: 14 days ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

simonpenel/thirdkind

Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels

Language: Rust - Size: 4.23 MB - Last synced: 2 days ago - Pushed: 2 months ago - Stars: 12 - Forks: 0

zxjsdp/nodefinder-go

Go implementation of NodeFinder program.

Language: Go - Size: 32.2 KB - Last synced: 16 days ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0

neherlab/nextclade_data_workflows

Language: Python - Size: 6.73 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 4 - Forks: 1

naturalis/barcode-constrained-phylogeny

Pipeline for building topologically-constrained phylogenies from DNA barcode data

Language: Python - Size: 3.32 MB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 1 - Forks: 3

neherlab/treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Language: Jupyter Notebook - Size: 10.3 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 204 - Forks: 55

clockor2/phylojs

Javascript library for manipulating phylogenetic trees

Language: TypeScript - Size: 5.03 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 5 - Forks: 1

vinuesa/get_phylomarkers

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

Language: Perl - Size: 118 MB - Last synced: 18 days ago - Pushed: 20 days ago - Stars: 46 - Forks: 8

beast-dev/beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees

Language: Java - Size: 152 MB - Last synced: 18 days ago - Pushed: 19 days ago - Stars: 176 - Forks: 69

albertyw/itolapi

Python API for the Interactive Tree of Life (iTOL)

Language: Python - Size: 684 KB - Last synced: 18 days ago - Pushed: 3 months ago - Stars: 31 - Forks: 10

Jaffar-Hussein/PhyloExplora

The project focuses on studying three extinct feline species from the American continent, analyzing ancient DNA sequences to uncover their evolutionary relationships with contemporary feline species. Implemented in C, the project involves parsing FASTA files, pairwise sequence alignment, and constructing phylogenetic trees using various algorithms.

Language: C - Size: 4.84 MB - Last synced: 19 days ago - Pushed: 4 months ago - Stars: 0 - Forks: 1

USDA-VS/vSNP

vSNP -- validate SNPs

Language: Python - Size: 68.5 MB - Last synced: 19 days ago - Pushed: over 1 year ago - Stars: 18 - Forks: 12

OpenOmics/mpox-seek

A rapid pipeline for targeted ONT monkeypox sequencing

Language: Python - Size: 661 KB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 1 - Forks: 0

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).

Language: Python - Size: 34.6 MB - Last synced: 4 days ago - Pushed: 9 months ago - Stars: 86 - Forks: 29

kris96tian/Phylogenetic_Tree_Generator

Web App for constructing phylogenetic trees using various clustering methods and algorithms.

Language: Python - Size: 12.7 KB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 0 - Forks: 0

mpxv-lineages/lineage-designation

Official place for proposals and details around monkeypox virus lineage designations

Language: Python - Size: 869 KB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 18 - Forks: 1

JLSteenwyk/orthosnap

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

Language: Python - Size: 112 MB - Last synced: 6 days ago - Pushed: 4 months ago - Stars: 19 - Forks: 1

ms609/TreeSearch

R package for phylogenetic tree search under custom optimality criteria

Language: R - Size: 117 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 5 - Forks: 4

ODiogoSilva/TriFusion

Streamlining phylogenomic data gathering, processing and visualization

Language: Python - Size: 100 MB - Last synced: 3 days ago - Pushed: over 5 years ago - Stars: 87 - Forks: 23

vshalisko/Phylogenetics

Stuff related to phylogenetics

Size: 16.6 KB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 1 - Forks: 0

d8vela/ColabSeq

ColabSeq: The one-stop shop for all of your multiple sequence analysis needs.

Language: Jupyter Notebook - Size: 402 KB - Last synced: 29 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

rrouz/AncFlow

AncFlow: A snakemake based pipeline for the ancestral sequence reconstruction of clustered phylogenetic subtrees.

Language: Python - Size: 4.64 MB - Last synced: 15 days ago - Pushed: 28 days ago - Stars: 1 - Forks: 0

iliapopov17/BI-Phylogenetics

Repository for accumulating the complete pipeline of phylogenetic studies

Language: Jupyter Notebook - Size: 21.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

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:

Language: C - Size: 45.3 MB - Last synced: 29 days ago - Pushed: 3 months ago - Stars: 217 - Forks: 78

AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Language: HTML - Size: 68.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 9 - Forks: 38

UBC-Stat-ML/nowellpack

Blang library for cancer genomics

Language: Xtend - Size: 2.48 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 6 - Forks: 3

lexedata/lexedata

Lexical Data Editing tools

Language: Python - Size: 42.7 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 5

Grice-Lab/HmmUFOtu

An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing

Language: C++ - Size: 53.3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 10 - Forks: 9

rasigadelab/thd

Time-scaled haplotypic density (THD) implementation for R. Estimates epidemic success from pathogen genetic data.

Language: R - Size: 518 KB - Last synced: about 1 month ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

YuLab-SMU/shinyTempSignal

Explore Temporal and Other Phylogenetic Signals

Language: R - Size: 1.28 MB - Last synced: 25 days ago - Pushed: about 2 months ago - Stars: 9 - Forks: 6

theosanderson/chronumental

Estimating time trees from very large phylogenies

Language: Python - Size: 2.47 MB - Last synced: 14 days ago - Pushed: 6 months ago - Stars: 23 - Forks: 4

raphael-group/scarlet

SCARLET (Single-cell Algorithm for Reconstructing Loss-supported Evolution of Tumors) is an algorithm that reconstructs tumor phylogenies from single-cell DNA sequencing data. SCARLET uses a loss-supported model that constrains mutation losses based on observed copy-number data.

Language: Limbo - Size: 287 KB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 7 - Forks: 4

mpieva/perl-ngs

Udo Stenzel's perl-ngs — a collection of Perl tools for next-generation sequencing [MIRROR]

Language: Perl - Size: 16.6 KB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

TreeBASE/supertreebase

Analysis of TreeBASE data through the NeXML API

Language: Perl - Size: 512 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 7 - Forks: 6

AntonelliLab/supersmartR-workshop-mini

Mini workshop introducing the supersmartR packages and pipeline

Language: R - Size: 14.7 MB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 1

AntonelliLab/cavvy-tree

:hamster: Building a tree of some small fluffy animals

Language: R - Size: 1.7 MB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 1

AntonelliLab/supersmartR

:eyeglasses::deciduous_tree: Towards a modular SUPERSMART pipeline in R

Size: 73.2 KB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 5 - Forks: 0

harmslab/topiary

Python framework for doing ancestral sequence reconstruction

Language: Python - Size: 60.9 MB - Last synced: 2 days ago - Pushed: about 1 year ago - Stars: 27 - Forks: 6

Zsailer/pyasr

Ancestral Sequence Reconstruction in Python

Language: Python - Size: 678 KB - Last synced: 2 days ago - Pushed: almost 5 years ago - Stars: 11 - Forks: 8

ropensci/RNeXML

Implementing semantically rich NeXML I/O in R

Language: R - Size: 8.53 MB - Last synced: 15 days ago - Pushed: over 1 year ago - Stars: 13 - Forks: 9

LorenaDerezanin/Tayra_Genome_Project

De novo genome assembly, phylogenetics, comparative genomics analysis, and functional variant annotation

Language: Shell - Size: 10.5 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

ropensci/beastier

R package to run BEAST2

Language: R - Size: 4.52 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 9 - Forks: 2

camayal/Some-Scripts

Repository for different one-file scripts (Phylogenetics, Bioinformatics, Name managers, etc.)

Language: Python - Size: 43.9 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

4ment/torchtree-physher

Language: Python - Size: 207 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

erathorn/MCPhylo.jl

(Hierarchical) Phylogenetic Models in Julia

Language: Julia - Size: 13.2 MB - Last synced: 25 days ago - Pushed: about 2 months ago - Stars: 7 - Forks: 2

molloy-lab/TREE-QMC-v2 📦

Species tree estimation from gene trees via quartets

Language: C++ - Size: 65.9 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

jananiravi/lectures-phylogeny_compgenomics

Supporting material for MMG 801 Lectures 3–5 on 'Phylogeny and Comparative Genomics'

Size: 1.6 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

sudorook/newick-tools

Process and visualize Newick-formatted phylogenetic trees.

Language: C - Size: 88.9 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

jamiemcg/BUSCO_phylogenomics

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

Language: Python - Size: 359 KB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 31 - Forks: 7

faridrashidi/trisicell

Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data

Language: Python - Size: 155 MB - Last synced: 5 days ago - Pushed: 4 months ago - Stars: 10 - Forks: 2

wiegertj/EBG

Tool for estimating the Felsenstein bootstrap support of phylogenetic trees

Language: Python - Size: 14.5 MB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 1 - Forks: 1

andersgs/harrietr 📦

An `R` package for various phylogenetic and evolutionary biology data manipulations

Language: R - Size: 454 KB - Last synced: 6 days ago - Pushed: about 6 years ago - Stars: 12 - Forks: 3