Base Classes and Functions for Phylogenetic Tree Input and Output
☆103Nov 1, 2025Updated 4 months ago
Alternatives and similar repositories for treeio
Users that are interested in treeio are comparing it to the libraries listed below
Sorting:
- A Tidy Tool for Phylogenetic Tree Data Manipulation☆57Jan 8, 2026Updated 2 months ago
- Visualization and annotation of phylogenetic trees☆922Mar 9, 2026Updated last week
- download files in R using wget -c☆16Aug 20, 2025Updated 7 months ago
- An R package that provides a base S4 class for comparative methods, incorporating one or more trees and trait data☆19Jan 30, 2024Updated 2 years ago
- Visualization tool for genetic reassortment☆21Nov 1, 2025Updated 4 months ago
- a complete reference book for treeio, tidytree and ggtree packages☆103Jul 13, 2022Updated 3 years ago
- Visualizing publication-quality multiple sequence alignment using ggplot2☆217Nov 1, 2025Updated 4 months ago
- Phylogenetic analysis in R☆213Mar 6, 2026Updated 2 weeks ago
- Taxonomy-aware DNA sequence processing toolkit☆33Feb 23, 2026Updated 3 weeks ago
- Fast alignment-free pangenome creation and exploration☆28Apr 16, 2020Updated 5 years ago
- Add Geom Layers On Circular Or Other Layout Tree Of “ggtree”☆96Jan 9, 2026Updated 2 months ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated last year
- ☆20Jun 15, 2024Updated last year
- Phylocom R interface☆15Apr 21, 2023Updated 2 years ago
- R interface to GenBank/GenPept files☆14Jan 12, 2021Updated 5 years ago
- Analysis of Phylogenetics and Evolution☆73Feb 18, 2026Updated last month
- This repo contains the code for a shiny app that allows for visualization of subset phylogenetic trees☆15Jan 9, 2019Updated 7 years ago
- Manage cached files☆23Jan 19, 2025Updated last year
- Bayesian Evolutionary Analysis by Sampling Trees☆268Jan 22, 2026Updated last month
- Inferring spatiotemporal dynamics of H5N1 influenza from sequence data☆10Sep 6, 2013Updated 12 years ago
- Repository for discussion lectures (MCBL121, Winter 2024), up until I decided that google slides was way easier.☆25Dec 17, 2024Updated last year
- ➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2☆584Jan 13, 2026Updated 2 months ago
- SYNPHONI is a tool designed for reconstructing the dynamic evolution of syntenic relationships across all scales of phylogenetic distance…☆12May 7, 2023Updated 2 years ago
- Drawing 'dendrogram' using 'ggtree'☆13Nov 1, 2025Updated 4 months ago
- ☆26Aug 25, 2021Updated 4 years ago
- Homepage for YuLab-SMU☆14Mar 6, 2026Updated 2 weeks ago
- TreeGrafter is a new software tool for annotating uncharacterized protein sequences, using annotated phylogenetic trees.☆13Mar 12, 2026Updated last week
- shell tools for processing phylogenetic trees☆119Aug 30, 2022Updated 3 years ago
- Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)☆11May 3, 2024Updated last year
- Visualization of Functional Enrichment Result☆257Mar 2, 2026Updated 2 weeks ago
- phylogenetics tools for linux (and other mostly posix compliant) computers☆123Jan 17, 2025Updated last year
- ☆15Feb 28, 2026Updated 2 weeks ago
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆82Updated this week
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆253Updated this week
- A very simple BLAST filtering pipeline☆19Mar 28, 2014Updated 11 years ago
- MeSH Enrichment and Semantic analyses☆12Dec 23, 2025Updated 2 months ago
- RAxML Next Generation: faster, easier-to-use and more flexible☆457Updated this week
- A grammar of graphics for comparative genomics☆748Feb 23, 2026Updated 3 weeks ago
- RPHAST: Phylogenetic Analysis with Space/Time Models in R☆13Nov 25, 2024Updated last year