Issues

• allow generate_nucleotides to only generate nucleotides for some mutation types?

  tskit-dev/pyslim#436 · Filter by author petrelharp opened on Aug 23, 2026
  1

• release tasks

  tskit-dev/pyslim#391 · Filter by author petrelharp opened on Aug 16, 2025
  1

• provide example of using individual parents

  tskit-dev/pyslim#386 · Filter by author petrelharp opened on Aug 12, 2025

• Add a citation manual

  tskit-dev/pyslim#377 · Filter by author hossam26644 opened on Jul 14, 2025

• add example of "add more mutations to SLiM sim"

  tskit-dev/pyslim#373 · Filter by author petrelharp opened on May 27, 2025
  3

• tools for multiple chromosome

  tskit-dev/pyslim#361 · Filter by author petrelharp opened on Feb 26, 2025
  9

• Potential to use .frequencies() method in /tutorial.html

  tskit-dev/pyslim#336 · Filter by author hyanwong opened on Nov 16, 2023

• test on annotating tsinfer'ed tree sequence

  tskit-dev/pyslim#317 · Filter by author petrelharp opened on Jun 26, 2023

• provide example of annotating existing mutations

  tskit-dev/pyslim#316 · Filter by author petrelharp opened on Jun 26, 2023

• tsinfered tree sequences don't have 'type' key in top-level metdata but set_tree_sequence_metadata expects they do

  tskit-dev/pyslim#315 · Filter by author petrelharp opened on Jun 25, 2023

• fixup XY annotation example

  documentationenhancement
  tskit-dev/pyslim#223 · Filter by author petrelharp opened on Dec 15, 2021 · v1.0

• test running .py files in SLiM recipes

  tests
  tskit-dev/pyslim#220 · Filter by author petrelharp opened on Dec 13, 2021 · v1.1
  3

• Vignettes as "tutorials" on tskit.dev/tutorials?

  tskit-dev/pyslim#212 · Filter by author hyanwong opened on Dec 7, 2021
  1

• use table.metadata_vector( ) in docs

  enhancement
  tskit-dev/pyslim#209 · Filter by author petrelharp opened on Nov 17, 2021 · v1.1

• add _X and _Y tests

  tests
  tskit-dev/pyslim#202 · Filter by author petrelharp opened on Sep 16, 2021 · v1.0

• tutorial for tracking lineages across space

  documentation
  tskit-dev/pyslim#195 · Filter by author petrelharp opened on Aug 25, 2021

• add citation.cff

  tskit-dev/pyslim#188 · Filter by author petrelharp opened on Jul 29, 2021

• add example of using "retain" in the tutorial

  tskit-dev/pyslim#152 · Filter by author petrelharp opened on Mar 5, 2021

• tutorial feature: spatial analysis

  documentation
  tskit-dev/pyslim#122 · Filter by author bhaller opened on Jan 12, 2021
  3

• add CI step that runs stdpopsim tests

  tests
  tskit-dev/pyslim#111 · Filter by author grahamgower opened on Dec 8, 2020 · v1.0
  2

  

• annotate_mutations

  enhancement
  tskit-dev/pyslim#103 · Filter by author petrelharp opened on Sep 16, 2020 · v1.1
  2

• a tree-sequence-validation feature inside pyslim would be useful

  tskit-dev/pyslim#62 · Filter by author bhaller opened on Jan 31, 2020 · v1.1
  4

• write method to emit SLiM reload script

  tskit-dev/pyslim#60 · Filter by author petrelharp opened on Jan 28, 2020 · v1.1
  1

• give example of matching individuals to something written to metadata

  documentation
  tskit-dev/pyslim#56 · Filter by author petrelharp opened on Nov 8, 2019
  2

• Provide spatial tools

  tskit-dev/pyslim#28 · Filter by author petrelharp opened on Jan 10, 2019