Python HyPhy: Facilitating HyPhy execution and parsing
☆21Dec 7, 2021Updated 4 years ago
Alternatives and similar repositories for phyphy
Users that are interested in phyphy are comparing it to the libraries listed below
Sorting:
- ☆20Jun 15, 2024Updated last year
- Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)☆19Oct 27, 2020Updated 5 years ago
- Manipulate genomic features and validate the syntax and reference sequence of your GFF3 files☆10Dec 26, 2022Updated 3 years ago
- HyPhy tutorials☆11Apr 9, 2018Updated 7 years ago
- Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework☆24Nov 29, 2022Updated 3 years ago
- Quality control for phylogenetic analyses☆13Feb 23, 2026Updated last week
- Explore spaces of phylogenetic trees☆29Aug 28, 2025Updated 6 months ago
- phylogenetic analyses informed by deep mutational scanning data☆15Jun 12, 2024Updated last year
- Automatically exported from code.google.com/p/prank-msa☆32Nov 17, 2025Updated 3 months ago
- A Windows Graphical Platform for Batch Manipulation of Tremendous Amount of Sequence Data☆30Apr 22, 2021Updated 4 years ago
- Quartet Sampling method for phylogenetic branch support evaluation☆19Feb 26, 2024Updated 2 years ago
- Bayesian molecular clock dating tutorial with genome-scale datasets☆19Dec 4, 2021Updated 4 years ago
- ggtree version of plotTree.R☆18Nov 12, 2018Updated 7 years ago
- Scripts for homology and orthology assessment from genomic sequences.☆19Oct 5, 2020Updated 5 years ago
- Software for detecting transposable element insertions from next-generation sequencing data☆14Mar 12, 2021Updated 4 years ago
- Posterior summarisation in Bayesian phylogenetics☆68Sep 27, 2025Updated 5 months ago
- ☆25Nov 29, 2022Updated 3 years ago
- Parallel implementation of OrthoMCL☆21Aug 26, 2022Updated 3 years ago
- Open source short linear motif discovery and sequence analysis☆26Sep 19, 2024Updated last year
- R client for Dryad web services☆26Jan 30, 2023Updated 3 years ago
- Datamonkey - Run state-of-the-art statistical models through the comfort of your browser☆10Feb 23, 2026Updated last week
- Perl script for manipulating multiple sequence alignments for phylogenetic reconstruction☆11Sep 29, 2014Updated 11 years ago
- stageR package☆13Feb 28, 2023Updated 3 years ago
- Estimate the cis-regulatory activity of transposable element (TEs) subfamilies☆10Dec 15, 2023Updated 2 years ago
- PartitionFinder discovers optimal partitioning schemes for DNA sequences.☆71Mar 10, 2021Updated 4 years ago
- Sweep Inference Framework (controlling for correlation)☆28Jul 10, 2024Updated last year
- ☆26Feb 24, 2026Updated last week
- Scalable relaxed clock phylogenetic dating☆28Sep 3, 2025Updated 6 months ago
- Automatically exported from code.google.com/p/densitree☆29Jul 27, 2025Updated 7 months ago
- This is a simple introductory tutorial to help you get started with using BEAST2 and its accomplices.☆11Jul 8, 2025Updated 7 months ago
- PAGAN2 multiple sequence aligner☆12Jul 2, 2024Updated last year
- ☆11Sep 16, 2021Updated 4 years ago
- GraphSNP: Using graph approach to investigate outbreak cluster and transmission in a web browser☆12Oct 5, 2025Updated 4 months ago
- QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics☆16Jan 12, 2026Updated last month
- akutils with massive updates over v1.1 to functionality and command line interface.☆15Jun 25, 2019Updated 6 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
- A multi-algorithmic framework for phylogenetic inference☆14Nov 28, 2025Updated 3 months ago
- Inference of putative transmission phylogenetic clusters☆12Oct 13, 2020Updated 5 years ago
- Whole organelle genome-wide alignment construction method, which ultilizes BLAST tool, to facilitate phylogeny analysis☆11May 7, 2018Updated 7 years ago