-
A population can have an activation time that is greater than zero -- for example, to sample ancient individuals. When using the demography debugger's `coalescence_rate_trajectory()` function, specif…
-
Some errors:
```
tests/test_vcf_examples.py:846:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _…
-
-
As discussed with @jeanrjc, for bacteria we need to use information in #848 to
- have individuals be haploid
- do gene conversion (for HGT)
(and circular chromosomes, but this isn't implemented…
-
As discussed in an msprime issue (https://github.com/tskit-dev/msprime/pull/1548#issuecomment-801165185) it would be useful to have a method to remove silent mutations.
Snags:
1. Which mutation d…
-
(This is related to #2024)
The docs for `recombination_rate` under `sim_ancestry` state:
```
See the [Recombination](https://tskit.dev/msprime/docs/stable/ancestry.html#sec-ancestry-recombinati…
-
There's going to be an awful lot of detail in the "Analysing trees" tutorial about fundamental operations like tree traversal. I wonder if we should hive that off into its own tutorial and reorganise …
-
To encourage people to think of tree sequences as graph objects, I think it would be helpful to add the graph representation to the "What is a Tree Sequence" tutorial, round about [here](https://tskit…
-
The ultimate goal of this project is to align *inferred* tree sequences to the pedigree graph. Therefore, we need to create tools to infer tree sequences from genetic samples.
I talked to @kobrica …
-
If there are different roots in different populations, then you can set things up so that `simulate(..., from_ts=ts)` has an infinite coalescence time (because of zero migration between populations), …