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popsim-consortium

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stdpopsim
A library of standard population genetic models

Python · 144 stars

Beginner friendly Everything

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update CI Open

popsim-consortium/stdpopsim#1865 · 1 comment · 1 assignee · Opened Sep 4, 2026
Create TraitsDebugger class Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

popsim-consortium/stdpopsim#1861 · 10 comments · Opened Aug 12, 2026
printing a contig gets "AttributeError: 'Contig' object has no attribute '_dfe_list'" Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

popsim-consortium/stdpopsim#1857 · 2 comments · Opened Jul 10, 2026
update top-level metadata Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

popsim-consortium/stdpopsim#1845 · Opened May 31, 2026
move back to release SLiM for CI after next SLiM release Open

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

popsim-consortium/stdpopsim#1841 · Opened May 29, 2026
Consolidate missing/unknown/masked regions in genetic/recombination maps Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 32/100

popsim-consortium/stdpopsim#1832 · 8 comments · Opened May 19, 2026
Should it be DME or DES? Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

popsim-consortium/stdpopsim#1830 · 5 comments · Opened Apr 30, 2026
write SLiM code for fitness functions Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

popsim-consortium/stdpopsim#1824 · Opened Mar 18, 2026
write SLiM code to construct traits Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

popsim-consortium/stdpopsim#1823 · Opened Mar 18, 2026
implement more multivariate distribution of trait effects Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

popsim-consortium/stdpopsim#1821 · Opened Mar 18, 2026
revsiit `contig.is_neutral()` method Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 64/100

popsim-consortium/stdpopsim#1820 · 1 comment · Opened Mar 18, 2026
move code that changes lognormal and uniform to Eidos to `slim_engine.py` Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 38/100

popsim-consortium/stdpopsim#1819 · Opened Mar 18, 2026
disallow rescaling for traits Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

popsim-consortium/stdpopsim#1818 · 5 comments · Opened Mar 18, 2026
Telomere region is not removed in SLiM simulation Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

popsim-consortium/stdpopsim#1812 · 8 comments · Opened Mar 8, 2026
Change additive models to independent dominance Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

popsim-consortium/stdpopsim#1808 · Opened Mar 3, 2026
allow/demosntrate smc(k) model Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

popsim-consortium/stdpopsim#1807 · Opened Mar 3, 2026
Question about migration rate units in EarlyWolfAdmixture_6F14 (Freedman et al. 2014) Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

popsim-consortium/stdpopsim#1801 · 8 comments · Opened Feb 19, 2026
revisit dominance set-up Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

popsim-consortium/stdpopsim#1799 · 1 comment · Opened Feb 11, 2026
Passing an msprime (or tskit) RateMap for a generic config Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 42/100

popsim-consortium/stdpopsim#1796 · 3 comments · Opened Feb 3, 2026
Saving stdpopsim outputs for some species/models/DFE for later reuse? Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

popsim-consortium/stdpopsim#1774 · Opened Nov 11, 2025
add additional properties to species and chromosomes Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

popsim-consortium/stdpopsim#1753 · Opened Sep 30, 2025
multiple chromosomes (eg with SLiM v5) Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

popsim-consortium/stdpopsim#1747 · 1 comment · Opened Sep 16, 2025
HapMapII_GRCh38 have zero-padding instead of missing data on the right flank Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

popsim-consortium/stdpopsim#1744 · 3 comments · Opened Aug 7, 2025
Drosophila recomb rates should be divided by two! Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

popsim-consortium/stdpopsim#1743 · 6 comments · Opened Jul 23, 2025
Polyploidy Polyploidy Polyploidy Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

popsim-consortium/stdpopsim#1742 · 6 comments · 3 reactions · Opened Jul 22, 2025
two DroMel recomb maps?!? Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

popsim-consortium/stdpopsim#1739 · 1 reaction · Opened Jun 10, 2025
QC for PosNeg_R24 (HomSap) Open

DFE QC

Difficulty 4/5 3-5 days Newbie friendliness 25/100

popsim-consortium/stdpopsim#1737 · Opened Jun 7, 2025
Unexpected warning in PanTro model Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

popsim-consortium/stdpopsim#1734 · 2 comments · Opened Jun 3, 2025
QC for {AlmondHist_1V16} ({Almond}) Open

Model QC

Difficulty 4/5 3-5 days Newbie friendliness 25/100

popsim-consortium/stdpopsim#1731 · 2 comments · Opened May 27, 2025
Almond Species Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

popsim-consortium/stdpopsim#1730 · 2 comments · Opened May 27, 2025
Adding traits to stdpopsim Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

popsim-consortium/stdpopsim#1725 · 9 comments · Opened Apr 29, 2025
Release 0.3.1 checklist Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

popsim-consortium/stdpopsim#1714 · Opened Mar 19, 2025
Add recombination map for SusScr (pig) Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

popsim-consortium/stdpopsim#1677 · 6 comments · Opened Feb 6, 2025
QC for GorillaGhost_5P23 (GorGor) Open

Model QC

Difficulty 4/5 3-5 days Newbie friendliness 25/100

popsim-consortium/stdpopsim#1660 · Opened Jan 20, 2025
Checks or warnings for assembly version and annotations and genetic maps Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

popsim-consortium/stdpopsim#1653 · 1 comment · Opened Jan 14, 2025
implement genome-wide both species h-s relationship DFE from Huber et al for AraTha Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

popsim-consortium/stdpopsim#1648 · Opened Jan 8, 2025
Do we have to review all models for specific mutation and recombination rates? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

popsim-consortium/stdpopsim#1631 · 2 comments · Opened Dec 23, 2024
Document output format in more detail Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

popsim-consortium/stdpopsim#1624 · Opened Dec 20, 2024
QC for HolsteinFriesian_1B16 (BosTau) Open

Model QC

Difficulty 4/5 3-5 days Newbie friendliness 35/100

popsim-consortium/stdpopsim#1598 · 12 comments · Opened Dec 12, 2024
Add Bos Indicus and Taurus model from Rossi et al. (2024) Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

popsim-consortium/stdpopsim#1590 · Opened Nov 3, 2024
should post-SLiM simplify have `keep_input_roots=True`? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

popsim-consortium/stdpopsim#1579 · 10 comments · Opened Jul 25, 2024
Release 0.3.0 checklist Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

popsim-consortium/stdpopsim#1565 · 4 comments · Opened Jul 1, 2024
document QC procedure for DFEs Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

popsim-consortium/stdpopsim#1557 · 1 comment · Opened Apr 16, 2024
orangutan model how to add adaptive introgression? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

popsim-consortium/stdpopsim#1554 · 1 comment · 1 reaction · Opened Mar 18, 2024
Mutation model Open

enhancement good first issue

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

popsim-consortium/stdpopsim#1546 · 1 comment · Opened Feb 16, 2024
Add detail about SLiM install to installation docs Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

popsim-consortium/stdpopsim#1541 · 2 comments · Opened Nov 16, 2023
test that requirements in `setup.cfg` are sufficient Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

popsim-consortium/stdpopsim#1518 · Opened Sep 18, 2023
Vignette on sampling parameter values Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

popsim-consortium/stdpopsim#1456 · 3 comments · Opened Mar 14, 2023
add info about type of data used to demographic model descriptions Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

popsim-consortium/stdpopsim#1442 · 1 comment · Opened Feb 17, 2023
Unable to verify if simulation is using specified model Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

popsim-consortium/stdpopsim#1435 · 2 comments · Opened Jan 26, 2023

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