A massively parallel tool for model selection and tree inference on thousands of genes
☆51Mar 4, 2024Updated 2 years ago
Alternatives and similar repositories for ParGenes
Users that are interested in ParGenes are comparing it to the libraries listed below
Sorting:
- Alignment-Based Sequence extraction☆15Feb 14, 2022Updated 4 years ago
- PREQUAL: a pre-alignment quality filter for comparative sequence analyses☆33Jun 1, 2022Updated 3 years ago
- ☆16Feb 20, 2024Updated 2 years ago
- A python tool for rapidly assessing the monophyly of user-defined groups in phylogenetic trees.☆10Apr 25, 2024Updated last year
- Manipulate and generate figures for trees in Newick format☆22Jul 31, 2025Updated 7 months ago
- Error correction for Illumina RNA-seq reads☆68Jan 4, 2026Updated 2 months ago
- an ensemble usage of MAFFT-linsi --add on large datasets☆13May 31, 2024Updated last year
- BOSTIn is a new, user-friendly phylogenetic artifact identification package.☆11Jan 20, 2026Updated 2 months ago
- ☆78Jun 2, 2025Updated 9 months ago
- RAxML Next Generation: faster, easier-to-use and more flexible☆457Updated this week
- Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.☆17Mar 18, 2019Updated 7 years ago
- software for UCE (and general) phylogenomics☆88Feb 27, 2026Updated 3 weeks ago
- Calculate summary statistics and manipulate multiple sequence alignments☆91Jan 28, 2026Updated last month
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆229Jan 4, 2026Updated 2 months ago
- This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MA…☆37Jan 3, 2026Updated 2 months ago
- Two-dimensional outlier detection algorithm for pinpointing errors in small species-specific stretches of the multiple sequence alignment…☆16May 27, 2024Updated last year
- Semi-Automatic Taxonomy Improvement and Validation Algorithm☆20Jan 8, 2024Updated 2 years ago
- Variant call verification☆16May 12, 2025Updated 10 months ago
- Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data☆37Apr 25, 2024Updated last year
- Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates…☆44Mar 7, 2024Updated 2 years ago
- spruceup☆25Aug 15, 2025Updated 7 months ago
- Accurate Species TRee ALgorithm☆275Apr 1, 2024Updated last year
- A mitogenome toolkit inspired by MitoZ, while being more effective, precise and flexible.☆20May 10, 2023Updated 2 years ago
- Best-fit model selection☆88Mar 21, 2024Updated last year
- A Windows Graphical Platform for Batch Manipulation of Tremendous Amount of Sequence Data☆30Apr 22, 2021Updated 4 years ago
- Tutorials on phylogenomic analyses for the ForBio Phylogenomics course☆38Mar 4, 2024Updated 2 years ago
- Support material for the "Comparative Genomics Laboratory" classes of the MSc in Biodiversity and Evolution at the University of Bologna.☆13Feb 27, 2026Updated 3 weeks ago
- ☆13Mar 12, 2026Updated last week
- A Python library for phylogenetic scripting, simulation, data processing and manipulation.☆233Jan 8, 2026Updated 2 months ago
- Detects and blacklists paralog RAD loci analyzed in Stacks or ipyrad, based on the McKinney 2017 method (doi:10.1111/1755-0998.12613)☆10Sep 4, 2019Updated 6 years ago
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆253Updated this week
- R and Python scripts used to simulate gene trees under coalescent model and detect gene flow using triple frequency☆15Dec 15, 2022Updated 3 years ago
- Alignment-free Phylogenetic Placement using filtered SPAced word Matches☆12Jul 19, 2023Updated 2 years ago
- Explore spaces of phylogenetic trees☆29Aug 28, 2025Updated 6 months ago
- a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference☆87Updated this week
- Visualizing gene tree conflict using Phyparts, and ETE3☆14Jun 17, 2023Updated 2 years ago
- de Bruijn graph cOrrectiOn from graph aLignment☆11Jul 20, 2020Updated 5 years ago
- shell tools for processing phylogenetic trees☆119Aug 30, 2022Updated 3 years ago
- Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.☆89Feb 19, 2026Updated last month