IQ-TREE version 3: software for phylogenetics
☆143Jun 25, 2026Updated last week
Alternatives and similar repositories for iqtree3
Users that are interested in iqtree3 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- The viral taxonomic assignment pipeline☆44Apr 16, 2026Updated 2 months ago
- Gene tree - species tree reconciliation from gene tree distributions☆42Apr 30, 2026Updated 2 months ago
- ☆93Updated this week
- PhyloBayes: phylogenetic reconstruction using infinite mixtures (CAT and CAT-GTR) -- serial version (for MPI, see pbmpi.git)☆15Oct 21, 2021Updated 4 years ago
- phylobayes mpi☆28Feb 3, 2023Updated 3 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- a broadly applicable tool for automated gene identification and retrieval☆42Jun 16, 2026Updated 2 weeks ago
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆249Updated this week
- Visualing species tree from ASTRAL with gene tree discordance☆33May 13, 2025Updated last year
- Scalable Maximum Likelihood Estimation of Phylogenetic Models☆26Mar 7, 2025Updated last year
- MetaSNV, a metagenomic SNV calling pipeline.☆21Mar 25, 2022Updated 4 years ago
- A phylogeny dating method using least-squares algorithms and criteria☆33Oct 25, 2024Updated last year
- A genome completeness evaluation tool based on miniprot☆248Jun 20, 2026Updated last week
- Quality control for phylogenetic analyses☆13May 25, 2026Updated last month
- A software for gap filling in genome assemblies☆10Aug 12, 2022Updated 3 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5☆89Mar 12, 2026Updated 3 months ago
- PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…☆199Jan 29, 2026Updated 5 months ago
- IQ-TREE software version 2: phylogenetics by maximum likelihood☆333Mar 12, 2026Updated 3 months ago
- ☆82May 2, 2026Updated last month
- Genome size estimation from long read overlaps☆92Jun 22, 2026Updated last week
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆23Mar 20, 2026Updated 3 months ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- FastOMA is a scalable software package to infer orthology relationship.☆99May 15, 2026Updated last month
- This is a repository for CAMPER.☆17Mar 18, 2024Updated 2 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- RegCloser is a genome gap-closing tool based on the robust regression approach, which is conceptually applicable to de novo assembly of N…☆15Apr 22, 2024Updated 2 years ago
- Multi-genome synteny block visualization tool☆59Jun 24, 2026Updated last week
- sunburst plots for taxonomy - working to update Krona☆44Sep 22, 2025Updated 9 months ago
- SplitsTree App☆128Updated this week
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated 3 weeks ago
- Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, e…☆284Apr 20, 2026Updated 2 months ago
- Efficient phylogenetic tree inference for massive taxonomic datasets☆145Apr 6, 2025Updated last year
- a short-read polishing tool for long-read assemblies☆218Sep 19, 2025Updated 9 months ago
- A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during…☆85Sep 8, 2025Updated 9 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆312Feb 3, 2026Updated 4 months ago
- Discovery of conserved gene clusters in multiple genomes☆134Jan 16, 2026Updated 5 months ago
- A hybrid assembly and MAG recovery pipeline (and more!)☆109Updated this week
- Tool for fully-automated inference of species trees from raw genome assemblies☆49May 30, 2026Updated last month
- Bayesian Evolutionary Analysis Sampling Trees☆245Updated this week
- Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.☆179Apr 6, 2026Updated 2 months ago
- A tool to filter BUSCO output into single-copy gene files for phylogenomics☆13Jul 24, 2024Updated last year