SimRA (Simulation based on Random-graphs Algorithms) is a framework for simulating generic and complex evolutionary scenarios of multiple populations with subdivision and admixture. The algorithm generates a network structure, called Ancestral Recombination Graph (ARG), that models coalescence and genetic exchange events (recombinations) with SN…
☆13Nov 28, 2022Updated 3 years ago
Alternatives and similar repositories for SimRA
Users that are interested in SimRA are comparing it to the libraries listed below
Sorting:
- A python framework for inferring demography from tracts of identity by state as reported in PLoS Genetics by Harris and Nielsen (2013)☆15Aug 1, 2013Updated 12 years ago
- Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)☆14May 1, 2023Updated 2 years ago
- G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual …☆34Apr 27, 2021Updated 4 years ago
- A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly☆11Feb 28, 2017Updated 9 years ago
- machine learning applications for dadi☆17Jan 23, 2025Updated last year
- Automated and Distributed Population Genetic Model Inference from Allele Frequency Spectra☆18Dec 4, 2025Updated 2 months ago
- A Hierarchical Softmax Framework for PyTorch☆22Jul 10, 2025Updated 7 months ago
- ArchaicSeeker is a series of software for detecting archaic introgression sequences and reconstructing introgression history. The latest …☆19Aug 6, 2025Updated 6 months ago
- Simple-to-use interactive comparison of two bacterial genomes☆25Jan 30, 2026Updated last month
- defiNETti is a program for performing Bayesian inference on exchangeable (or permutation-invariant) data via deep learning. In particula…☆20Apr 10, 2018Updated 7 years ago
- Large scale ancestry inference from PCA data☆23May 2, 2023Updated 2 years ago
- Accelerated Bayesian inference of population size history from whole genome data.☆33Sep 29, 2025Updated 5 months ago
- Tools for dealing with tree sequences coming to and from SLiM.☆28Dec 20, 2025Updated 2 months ago
- Estimation of population genetic parameters using deep learning☆29Apr 2, 2025Updated 10 months ago
- Scripts for processing single liver cells RNA-Seq 10X Genomics Data☆26Oct 17, 2018Updated 7 years ago
- shifts hg19/38 genomic position for feasible input format.☆12Jun 8, 2023Updated 2 years ago
- Detection and classification selective sweep use domain adaptive model☆10Apr 29, 2024Updated last year
- ☆33Nov 11, 2025Updated 3 months ago
- Wavefront alignment algorithm (WFA) in Golang☆32Jul 26, 2025Updated 7 months ago
- Scripts of population genomics analysis☆36May 8, 2018Updated 7 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- An Efficient Swiss Army Knife for Population Genomic Analyses in R☆38May 21, 2024Updated last year
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆41Apr 17, 2024Updated last year
- RIESLING: Super-enhancer identification. (Rapid Identification of EnhancerS LInked to Nearby Genes)☆10Jun 28, 2018Updated 7 years ago
- Functions for handling RNA-seq files and formats as input and output for scrattch functions.☆11Aug 20, 2025Updated 6 months ago
- INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation dataset…☆12Dec 12, 2022Updated 3 years ago
- m(6)A methylation analysis☆10Mar 9, 2019Updated 6 years ago
- Filters for Next Generation Sequencing☆12Oct 31, 2024Updated last year
- Chromosome Scale Assembler: A high-throughput chromosome scale genome assembly pipeline for vertebrate genomes☆10Oct 16, 2024Updated last year
- Supporting information of 'Single-cell RNA sequencing of a European and an African lymphoblastoid cell line'☆10Feb 27, 2020Updated 6 years ago
- RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors☆37Nov 15, 2023Updated 2 years ago
- Sparse Convolutional Denoising Autoencoders for Genotype Imputation☆13Aug 23, 2019Updated 6 years ago
- A Python package for landscape genomic simulation☆12Dec 15, 2025Updated 2 months ago
- This is a tool to estimate pairwise relatedness from ancient DNA, taking in account contamination, ROH, ascertainment bias.☆14Aug 6, 2024Updated last year
- ☆10Mar 29, 2025Updated 11 months ago
- A transformer model to predict pathogenic mutations☆12Jun 25, 2025Updated 8 months ago
- ☆13Feb 27, 2024Updated 2 years ago
- Bioinformatics / Explore oligonucleotide composition similarity between assembly contigs or scaffolds to detect contaminant DNA.☆12Feb 27, 2019Updated 7 years ago
- This repo is archived, the these workflows are still available in the GATK repository under the scripts directory. The workflows are also…☆11Mar 9, 2020Updated 5 years ago