Alternatives and similar repositories for icytree

Users that are interested in icytree are comparing it to the libraries listed below

• nmatzke / BEASTmasteR

  View on GitHub
  R code for writing Beast2 XML (especially morphology/tip-dating)
  ☆11Jun 26, 2024Updated last year
• nextstrain / zika-tutorial

  View on GitHub
  Data and scripts for Zika virus tutorial
  ☆10Oct 14, 2025Updated 3 months ago
• quick-lab / SARS-CoV-2

  View on GitHub
  SARs-CoV-2 Primer schemes
  ☆16May 14, 2025Updated 8 months ago
• maximilianh / multiSub

  View on GitHub
  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…
  ☆36May 1, 2022Updated 3 years ago
• phylogeography / spread

  View on GitHub
  Spread visualizes how viruses and other pathogens are spreading in time and space. It creates compellable shareable, interactive and time…
  ☆19Jan 23, 2025Updated last year
• vibbits / phyd3

  View on GitHub
  Phylogenetic tree viewer based on D3.js
  ☆61Aug 16, 2024Updated last year
• revbayes / RevGadgets

  View on GitHub
  Postprocessing gadgets for output generated by RevBayes
  ☆14Feb 6, 2026Updated last week
• pinbo / msa2snp

  View on GitHub
  SNP and indel calls from multiple sequence alignment (MSA)
  ☆13Nov 11, 2022Updated 3 years ago
• liamrevell / learnPopGen

  View on GitHub
  initial commit
  ☆26Dec 29, 2022Updated 3 years ago
• mrborges23 / delta_statistic

  View on GitHub
  Codes for calculating delta, a phylogenetic analog of the Shannon entropy for measuring the degree of phylogenetic signal between a categ…
  ☆25Jun 16, 2021Updated 4 years ago
• acorg / figtree-recolor

  View on GitHub
  A script to re-color a FigTree saved Nexus file
  ☆13Jan 29, 2017Updated 9 years ago
• yiq / SubcloneSeeker

  View on GitHub
  Computational Framework to reconstructing tumor clone structures
  ☆15Mar 31, 2021Updated 4 years ago
• raphael-group / multibreak-sv

  View on GitHub
  MultiBreak-SV identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combin…
  ☆12Jul 19, 2016Updated 9 years ago
• yatisht / strain_phylogenetics

  View on GitHub
  Tools for analyzing and comparing SARS-CoV-2 phylogenies
  ☆10Nov 21, 2020Updated 5 years ago
• bayesiancook / coevol

  View on GitHub
  coevol -- Correlated evolution of substitution rates and quantitative traits
  ☆13Oct 18, 2024Updated last year
• emvolz / treedater

  View on GitHub
  Scalable relaxed clock phylogenetic dating
  ☆28Sep 3, 2025Updated 5 months ago
• rbouckaert / DensiTree

  View on GitHub
  Automatically exported from code.google.com/p/densitree
  ☆29Jul 27, 2025Updated 6 months ago
• trvrb / flux

  View on GitHub
  Integrating influenza antigenic dynamics with molecular evolution
  ☆12May 28, 2015Updated 10 years ago
• whitlock / OutFLANK

  View on GitHub
  A procedure to find Fst outliers based on an inferred distribution of neutral Fst
  ☆19Aug 26, 2019Updated 6 years ago
• lauterbur / Flex-sweep

  View on GitHub
  Versatile tool for detecting selective sweeps with a variety of ages, strengths, starting allele frequencies, and completeness.
  ☆15Mar 1, 2024Updated last year
• rbouckaert / Babel

  View on GitHub
  BEAST analysis backing effective linguistics
  ☆12May 4, 2025Updated 9 months ago
• PierreBarrat / TreeKnit.jl

  View on GitHub
  TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).
  ☆14Feb 18, 2025Updated 11 months ago
• mills-lab / dinumt

  View on GitHub
  ☆14Oct 29, 2021Updated 4 years ago
• enasequence / read_docs

  View on GitHub
  ☆13Jan 8, 2026Updated last month
• camilogarciabotero / biocomp-book

  View on GitHub
  A repo hosting the combined lectures of a course on Fundamentals of Computational Biology
  ☆14Jul 4, 2023Updated 2 years ago
• heibl / ips

  View on GitHub
  R Interfaces to Phylogenetic Software
  ☆12Sep 15, 2025Updated 4 months ago
• flu-crew / octoFLU

  View on GitHub
  Script that labels phylogenetic clades based on the clade of the nearest neighbor using patristic distances determined from the tree.
  ☆15Dec 11, 2024Updated last year
• JH-Zhou / HandyCNV

  View on GitHub
  An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH
  ☆15Oct 17, 2021Updated 4 years ago
• LeilyR / Multi-genome-Reference

  View on GitHub
  A program to generate a graph which presents a simplified representation of several full length genomes
  ☆13Aug 23, 2018Updated 7 years ago
• lh3 / fermi

  View on GitHub
  A WGS de novo assembler based on the FMD-index for large genomes
  ☆74Dec 6, 2013Updated 12 years ago
• lauguma / GWideCodeML

  View on GitHub
  A Python package for testing evolutionary hypotheses in genome-wide approaches.
  ☆33Mar 5, 2021Updated 4 years ago
• jacahill / hPSMC

  View on GitHub
  Tools for F1 hybrid PSMC (hPSMC) divergence time inference from whole genomes
  ☆14May 29, 2024Updated last year
• davidrasm / Espalier

  View on GitHub
  Espalier is a Python package for working with discordant phylogenetic trees using maximum agreement forests.
  ☆14Jul 19, 2023Updated 2 years ago
• jasom / pdfparse

  View on GitHub
  Port of Python's pdfminer to Lisp
  ☆15Jan 30, 2016Updated 10 years ago
• lexibank / acd

  View on GitHub
  Austronesian Comparative Dictionary
  ☆16Jan 7, 2025Updated last year
• dlce-eva / python-nexus

  View on GitHub
  python-nexus - Generic nexus (.nex, .trees) reader/writer for python
  ☆11Feb 20, 2025Updated 11 months ago
• kstatebioinfo / Irys-scaffolding

  View on GitHub
  scripts to parse IrysView output
  ☆11Jun 24, 2015Updated 10 years ago
• mossmatters / MJPythonNotebooks

  View on GitHub
  Visualizing gene tree conflict using Phyparts, and ETE3
  ☆14Jun 17, 2023Updated 2 years ago
• BrendelGroup / SRAssembler

  View on GitHub
  Selective and Recursive local Assembler
  ☆15Jan 31, 2022Updated 4 years ago