IQ-TREE software version 2: phylogenetics by maximum likelihood
☆334Mar 12, 2026Updated 4 months ago
Alternatives and similar repositories for iqtree2
Users that are interested in iqtree2 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- RAxML Next Generation: faster, easier-to-use and more flexible☆472Jul 6, 2026Updated 2 weeks ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆254Jul 14, 2026Updated last week
- PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…☆200Jan 29, 2026Updated 5 months ago
- A genome completeness evaluation tool based on miniprot☆254Updated this week
- An updated pipeline for pangenome investigation☆365Jul 2, 2026Updated 2 weeks ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Efficient phylogenomic software by maximum likelihood☆210Nov 4, 2021Updated 4 years ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆221Aug 27, 2025Updated 10 months ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆663Jul 10, 2026Updated last week
- Synteny and Rearrangement Identifier☆480Jul 1, 2026Updated 2 weeks ago
- Efficient phylogenetic tree inference for massive taxonomic datasets☆146Apr 6, 2025Updated last year
- Align proteins to genomes with splicing and frameshift☆408Jan 5, 2026Updated 6 months ago
- SPAdes Genome Assembler☆953Jun 16, 2026Updated last month
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆189Mar 17, 2026Updated 4 months ago
- Create a tree using Mash distances☆188Oct 24, 2023Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆124Jun 2, 2026Updated last month
- An accurate GFF3/GTF lift over pipeline☆547Aug 1, 2023Updated 2 years ago
- Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis☆339Jul 7, 2023Updated 3 years ago
- A grammar of graphics for comparative genomics☆774Jul 3, 2026Updated 2 weeks ago
- IQ-TREE version 3: software for phylogenetics☆146Updated this week
- a short-read polishing tool for long-read assemblies☆218Sep 19, 2025Updated 10 months ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆241Dec 29, 2023Updated 2 years ago
- a Bioinformatics Application for Navigating De novo Assembly Graphs Easily☆672Jul 7, 2026Updated 2 weeks ago
- A user-friendly workflow for phylogenomics☆231Updated this week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Genome annotation with AUGUSTUS☆336May 30, 2026Updated last month
- Pairwise SNP distance matrix from a FASTA sequence alignment☆156Dec 31, 2025Updated 6 months ago
- Gene cluster comparison figure generator☆648Dec 22, 2025Updated 7 months ago
- A Python library that exposes features from IQ-TREE - efficient software for phylogenomic inference☆49Updated this week
- Fast Whole-Genome Similarity (ANI) Estimation☆470Dec 16, 2025Updated 7 months ago
- Gotree: a set of command line tools and an API to manipulate phylogenetic trees.☆150Updated this week
- Assemble bacterial isolate genomes from Nanopore reads☆136Jan 22, 2025Updated last year
- Mummer alignment tool☆565Feb 4, 2025Updated last year
- Split k-mer analysis – version 2☆105Jul 9, 2026Updated last week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics☆208Aug 25, 2025Updated 10 months ago
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆267Updated this week
- Phylogenetic orthology inference for comparative genomics☆865Jul 15, 2025Updated last year
- Tool to plot synteny and structural rearrangements between genomes☆349Apr 7, 2025Updated last year
- Pan-genome wide association studies☆219May 29, 2024Updated 2 years ago
- Eukaryotic Genome Annotation Pipeline☆393Jul 12, 2026Updated last week
- ☆349Mar 4, 2025Updated last year