Espalier is a Python package for working with discordant phylogenetic trees using maximum agreement forests.
☆14Jul 19, 2023Updated 2 years ago
Alternatives and similar repositories for Espalier
Users that are interested in Espalier are comparing it to the libraries listed below
Sorting:
- initial commit☆26Dec 29, 2022Updated 3 years ago
- Modification of BayesAss 3.0.4 to allow handling of large SNP datasets☆17Feb 19, 2022Updated 4 years ago
- Simple scripts for concatenate alignments and rename terminals for phylogenetics☆22Sep 20, 2022Updated 3 years ago
- ☆12Feb 16, 2025Updated last year
- Postprocessing gadgets for output generated by RevBayes☆14Feb 22, 2026Updated last week
- Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning☆12Feb 6, 2026Updated 3 weeks ago
- Differential quantification of alternative splicing events on spliced pangenome graphs☆15Jan 30, 2026Updated last month
- CPANG19 - Computational PANGenomics (2019)☆12May 7, 2020Updated 5 years ago
- Inference of putative transmission phylogenetic clusters☆12Oct 13, 2020Updated 5 years ago
- HaploSweep is a method for detecting and categorizing soft and hard selective sweeps based on haplotype structure.☆11Sep 24, 2024Updated last year
- Haplotype and population structure inference using neural networks.☆28Dec 5, 2024Updated last year
- Haplotype-aware genome assembly toolkit☆30Jan 8, 2020Updated 6 years ago
- ☆12May 6, 2022Updated 3 years ago
- A program to generate a graph which presents a simplified representation of several full length genomes☆13Aug 23, 2018Updated 7 years ago
- A reliable gap filling pipeline for draft genomes☆11Sep 17, 2019Updated 6 years ago
- Extract metadata from biosamples in NCBI☆17Apr 12, 2021Updated 4 years ago
- ☆15Updated this week
- An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH☆15Oct 17, 2021Updated 4 years ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Program for estimating dN/dS in overlapping genes (OLGs)☆14Dec 2, 2022Updated 3 years ago
- MCMCtreeR: A package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree☆45Nov 21, 2019Updated 6 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆68Feb 23, 2026Updated last week
- Fast and accurate Phylogeny estimation with self-attention Networks☆42Apr 19, 2025Updated 10 months ago
- Multivariate vIsualisatioN and OuTlier Analysis Using R☆14Apr 8, 2023Updated 2 years ago
- ☆17Feb 27, 2026Updated last week
- GCtree: phylogenetic inference of genotype-collapsed trees☆18Aug 27, 2024Updated last year
- An Efficient Swiss Army Knife for Population Genomic Analyses in R☆38May 21, 2024Updated last year
- Repository containing a method for automatically identifying pathogen lineages from a phylogeny.☆17May 19, 2023Updated 2 years ago
- Python package for detecting positive selective sweeps using time-series genomics sampling data.☆19Apr 9, 2024Updated last year
- Tool for modelling of mitochondrial heteroplasmy☆20Jul 16, 2024Updated last year
- Fast and frugal disk based k-mer counter☆14Apr 1, 2021Updated 4 years ago
- ☆18Jun 11, 2024Updated last year
- a versatile toolkit for processing and analyzing diverse types of sequence data☆22Feb 18, 2026Updated 2 weeks ago
- ☆21Dec 30, 2025Updated 2 months ago
- Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates☆21Nov 8, 2024Updated last year
- Spatial Phylogenetic Reconstruction of Evolutionary Dynamics 3☆17Apr 28, 2023Updated 2 years ago
- Maximum a posteriori estimate of contamination for ancient samples☆23Nov 4, 2025Updated 4 months ago
- Fast and accurate tool for estimating genomic distances between genome-skims☆47Sep 28, 2023Updated 2 years ago
- ☆18Dec 15, 2021Updated 4 years ago