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Search results for population genetics
population-genetics
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53 search results found
Anvio
⭐
396
An analysis and visualization platform for 'omics data
Glow
⭐
251
An open-source toolkit for large-scale genomic analysis
Vcfr
⭐
225
Tools to work with variant call format files
Psmc
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120
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
Eager
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112
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Pophelper
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106
An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.
Snpgenie
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94
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
Grenepipe
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75
A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.
Poppunk
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71
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
Vcf2dis
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67
VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format
Poppr
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65
🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
Genesis
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54
A library for working with phylogenetic and population genetic data.
Diploshic
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47
feature-based deep learning for the identification of selective sweeps
Slendr
⭐
46
Population genetic simulations in R 🌍
Neural Admixture
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44
Rapid population clustering with autoencoders
Mixer
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41
Causal Mixture Model for GWAS summary statistics
Tomahawk
⭐
39
Fast calculations of linkage-disequilibrium in large-scale human cohorts
Get_phylomarkers
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39
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
Ldlinkr
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30
LDlinkR
Admixr
⭐
25
An R package for reproducible and automated ADMIXTOOLS analyses
Locator
⭐
25
deep learning prediction of geographic location from individual genome sequences
Fwdpy11
⭐
25
Forward-time simulation in Python using fwdpp
Panpop
⭐
24
Application of pan-genome for population
Pcaone
⭐
24
Principal Component Analysis All in One
Hierfstat
⭐
22
the hierfstat package
Stratag
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22
strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
Nci Webtools Dceg Linkage
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20
LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups. Each included application is specialized for querying and displaying unique aspects of linkage disequilibrium.
Isafe
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19
Pinpoints the mutation favored by selection
Grenedalf
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18
Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments
Rhierbaps
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17
rhierbaps: R implementation of hierBAPS
Rna Seq Pop
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17
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
Angsd Wrapper
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13
Utilities for analyzing next generation sequencing data.
Timesweeper
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12
Python package for detecting positive selective sweeps using time-series genomics sampling data.
Kgp
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12
1000 Genomes Project Metadata R Package
Scripts
⭐
11
Random scripts, mostly for dealing with RADseq data and DNA sequence alignments
Stormbitmaps
⭐
11
Fast algorithms for computing XX^T for binary matrices
Starmie
⭐
10
starmie: plotting and inference for population structure models 🌟
Kakapo
⭐
10
Scripts and code for Kākāpō genomic data
Vcfpp
⭐
9
a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.
Polyploid Genotyping
⭐
8
SNP genotyping in polyploids
Eems Around The World
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8
Repo to analyze population genetic data with many different methods
Happe
⭐
8
A tool to visualize the haplotype pattern and various information in excel.
Ku Popgen2022
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8
Lecture notes and materials on simulations for the 2022 popgen course at Copenhagen University
Course R Mol Data
⭐
8
R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.
Popgen
⭐
7
Small scripts for population genetics analysis
Admixfrog
⭐
7
Popgen Docker
⭐
6
Dockerfile(s) for population genetics
Geno4sd
⭐
6
An python omics data toolkit for the analysis across biological scales
Mitobench
⭐
6
The mitochondrial workbench
Opp Op Pop Init
⭐
6
PyPI package containing opposition learning operators and population initializers for evolutionary algorithms
Angry Moran Simulator
⭐
5
A general game-theoretical framework to carry out scientific simulations of populations' evolution according to the Moran model 🧮
Mycorrhiza Algorithm
⭐
5
Combining phylogenetic networks and Random Forests for prediction of ancestry from multilocus genotype data
Tarca
⭐
5
TarCA is an R package used for inferring the number of progenitors of the focal cell population based on the cell phylogeny.
1-53 of 53 search results
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