GitPlanet

Cheap and reliable Node.js hosting starts at $3/month, and $1/month static HTML hosting

Created with love in Canada, visit hostnodejs.com today

Feel like to post an Ad? Learn Details
All Projects → molpopgen → fwdpy11

molpopgen / fwdpy11

Licence: GPL-3.0 license
Forward-time simulation in Python using fwdpp

Programming Languages

python
139335 projects - #7 most used programming language
C++
36643 projects - #6 most used programming language
CMake
9771 projects
rust
11053 projects
Dockerfile
14818 projects
shell
77523 projects

Labels

genomicsgeneticssimulationpopulation-geneticstree-sequences

Projects that are alternatives of or similar to fwdpy11

genipe
Genome-wide imputation pipeline
Stars: ✭ 28 (+12%)
Mutual labels:  genomics, genetics
graphsim
R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)
Stars: ✭ 16 (-36%)
Mutual labels:  genomics, genetics
manhattan generator
Manhattan plot Generator
Stars: ✭ 20 (-20%)
Mutual labels:  genomics, genetics
region-plot
A tool to plot significant regions of GWAS
Stars: ✭ 20 (-20%)
Mutual labels:  genomics, genetics
get phylomarkers
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches
Stars: ✭ 34 (+36%)
Mutual labels:  genomics, population-genetics
HumanIdiogramLibrary
Resource of human chromosome schematics & images
Stars: ✭ 76 (+204%)
Mutual labels:  genomics, genetics
dee2
Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
Stars: ✭ 32 (+28%)
Mutual labels:  genomics, genetics
awesome-genetics
A curated list of awesome bioinformatics software.
Stars: ✭ 60 (+140%)
Mutual labels:  genomics, genetics
psmc
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
Stars: ✭ 121 (+384%)
Mutual labels:  genomics, population-genetics
OpenOmics
A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.
Stars: ✭ 22 (-12%)
Mutual labels:  genomics
human genomics pipeline
A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
Stars: ✭ 19 (-24%)
Mutual labels:  genomics
CuteVCF
simple viewer for variant call format using htslib
Stars: ✭ 30 (+20%)
Mutual labels:  genomics
nthash
ntHash implementation in Rust
Stars: ✭ 26 (+4%)
Mutual labels:  genomics
omxware-getting-started
Examples to get started with IBM Functional Genomics Platform
Stars: ✭ 13 (-48%)
Mutual labels:  genomics
bap
Bead-based single-cell atac processing
Stars: ✭ 20 (-20%)
Mutual labels:  genomics
vrs-python
GA4GH Variation Representation Python Implementation
Stars: ✭ 35 (+40%)
Mutual labels:  genomics
cryfa
A secure encryption tool for genomic data
Stars: ✭ 53 (+112%)
Mutual labels:  genomics
phenol
phenol: Phenotype ontology library
Stars: ✭ 15 (-40%)
Mutual labels:  genomics
gnomad-browser
Explore gnomAD datasets on the web
Stars: ✭ 61 (+144%)
Mutual labels:  genomics
CUT-RUNTools-2.0
CUT&RUN and CUT&Tag data processing and analysis
Stars: ✭ 36 (+44%)
Mutual labels:  genomics
View All Similar Projects ➔

fwdpy11

This is the README for fwdpy11, which is a Python package for forward-time population genetic simulation. It uses fwdpp as its C++ back-end.

Build status

Main:

https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=main https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=main

Development:

https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=dev https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=dev

Miscellaneous

Python code style:

Features

  • Pickle-able population objects
  • Parallel computation via multiprocessing or concurrent.futures.
  • Custom temporal samplers to analyze populations during a simulation may be written in pure Python.
  • Flexible interface for simulating models with multiple populations.

Documentation

The manual can be found here.

License

GPLv3 or later (See COPYING)

Supported Python version

fwdpy11 is written for Python 3. We will not modify the package to be compatible with Python 2.7.

Dependencies and installation

These topics are covered in the user manual:

Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].