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Population Genetics Python Packages

Python packages with the GitHub topic population-genetics. Sorted by relevance, with stars and monthly downloads.
molpopgen
fwdpy11

Forward-time simulation in Python using fwdpp

7K 32 6
AI-sandbox
adamixture

Fast population clustering with Adam-EM Optimization.

6K 23 1
polyactis
palos

Misc Python modules developed and used by the yfish group

3K 0 0
PasaOpasen
oppoppopinit

PyPI package containing opposition learning operators and population initializers for evolutionary algorithms

2K 6 2
AI-sandbox
neural-admixture

Rapid population clustering with autoencoders

2K 86 11
jyzhu-pointless
natal-core

Numba-Accelerated Toolkit for Analysis of Lifecycles

1K 3 1
kr-colab
diploshic

A deep learning tool for identifying hard and soft selective sweeps in population genomic data

824 59 17
remytuyeras
haplodynamics

A python library to develop genomic data simulators

606 4 0
jgeofil
mycorrhiza

Combining phylogenetic networks and Random Forests for prediction of ancestry from multilocus genotype data

514 8 2
KalinNonchev
gnomad-db

Scalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and WES.

403 52 12
SchriderLab
timesweeper

Python package for detecting positive selective sweeps using time-series genomics sampling data.

376 20 2
not-a-feature
tajimas-d

Compute the Tajima's-D, Pi-Estimator or Watterson-Estimator for multiple sequences.

315 7 0
jfmao
graphmana

Graph-native data management platform for variant genomics

310 3 0
johnlees
poppunk

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

310 108 22
jfmao
graphpop-cli

GraphPop is a population genomics platform that replaces the flat-file, matrix-based paradigm with a graph-native architecture.

305 3 0
kkokay07
laax

Repository for population genetics and quantitative genetics metrics implementarion and visualization

85 2 0
AngryMaciek
moranpycess

A general game-theoretical framework to carry out scientific simulations of populations' evolution according to the Moran model 🧮

70 6 6
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