Fast and flexible code for solving the inverse Ising/Potts inference problem
☆27May 12, 2023Updated 2 years ago
Alternatives and similar repositories for ACE
Users that are interested in ACE are comparing it to the libraries listed below
Sorting:
- Graphical Representation of Ancestral Sequence Predictions☆12Mar 6, 2023Updated 2 years ago
- Phylogenetic pathway–dependent recognition of fixed substitutions and parallel mutations☆11Sep 18, 2025Updated 5 months ago
- Postprocessing gadgets for output generated by RevBayes☆14Feb 22, 2026Updated last week
- Software to process, statistically analyse and visualise deep mutational scanning data☆14Oct 29, 2025Updated 4 months ago
- Isomorphisms of quiver representations applied to neural networks.☆16Jul 25, 2024Updated last year
- Calculate indel trajectory likelihoods using methods of Miklós, Lunter & Holmes (2004), De Maio (2020), and Holmes (2020)☆14Sep 17, 2022Updated 3 years ago
- Nextflow pipeline for the computation of structure-based MSAs with AlphaFold2 models☆12Dec 20, 2022Updated 3 years ago
- Faster, more accurate and entirely open source method for predicting contacts in proteins☆12May 21, 2018Updated 7 years ago
- An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH☆15Oct 17, 2021Updated 4 years ago
- Espalier is a Python package for working with discordant phylogenetic trees using maximum agreement forests.☆14Jul 19, 2023Updated 2 years ago
- Contact map alignment☆16May 10, 2018Updated 7 years ago
- Code for analyzing multi-electrode array recordings (spikes & LFP) for Trujillo, Gao, Negraes et al., 2019.☆16Apr 23, 2020Updated 5 years ago
- GCtree: phylogenetic inference of genotype-collapsed trees☆18Aug 27, 2024Updated last year
- ☆18Nov 18, 2025Updated 3 months ago
- Modification of BayesAss 3.0.4 to allow handling of large SNP datasets☆17Feb 19, 2022Updated 4 years ago
- Repository containing a method for automatically identifying pathogen lineages from a phylogeny.☆17May 19, 2023Updated 2 years ago
- Pipeline to detect HLA disruption from WES and RNAseq data☆22Feb 17, 2025Updated last year
- Summary statistics for repertoires☆17Feb 1, 2023Updated 3 years ago
- This repository presents a global overview of why GitHub, and especially Git+R should be used by everyone, helping for reproducibility. T…☆18Jun 12, 2025Updated 8 months ago
- Epidemiological modeling framework for pathogen population genetics and evolution.☆18Oct 7, 2024Updated last year
- a versatile toolkit for processing and analyzing diverse types of sequence data☆22Feb 18, 2026Updated last week
- Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)☆19Oct 27, 2020Updated 5 years ago
- HLA-I ligand predictor☆43Sep 24, 2025Updated 5 months ago
- Annotate sequences from BLAST against KEGG DB with KO numbers and summarize them in KEGG modules.☆22Dec 27, 2018Updated 7 years ago
- HLA-II ligand predictor.☆46Apr 6, 2023Updated 2 years ago
- Multivariate Gaussian Direct Coupling Analysis for residue contact prediction in protein families - Julia module☆22Jan 27, 2022Updated 4 years ago
- A Full Featured Multiple Sequence Alignment Editor.☆26May 21, 2018Updated 7 years ago
- ☆16Aug 17, 2023Updated 2 years ago
- An R package with toolkits for tong's friends☆11Mar 18, 2025Updated 11 months ago
- Statistical_IV: J-Divergence Hypothesis Test for the Information Value (IV)☆11May 18, 2025Updated 9 months ago
- Scalable relaxed clock phylogenetic dating☆28Sep 3, 2025Updated 5 months ago
- Automatically exported from code.google.com/p/densitree☆29Jul 27, 2025Updated 7 months ago
- Taxonomy-aware DNA sequence processing toolkit☆33Updated this week
- 🍶 Genome assembly with short sequence reads☆25Jan 21, 2024Updated 2 years ago
- A phylogeny dating method using least-squares algorithms and criteria☆32Oct 25, 2024Updated last year
- MARS: improving Multiple circular sequence Alignment using Refined Sequences☆31May 2, 2025Updated 9 months ago
- This project aims at designing an easy self-made ultrasound imaging device. It mainly consists of "Phased-array transducer", "Pulse-contr…☆14Jun 28, 2023Updated 2 years ago
- ♥ Fast and Accurate Estimation of Evolutionary Distances☆29Apr 14, 2025Updated 10 months ago
- A Python package for testing evolutionary hypotheses in genome-wide approaches.☆33Mar 5, 2021Updated 4 years ago