Yan Wong
It might be useful for `resolve_polytomies` to return the number of polytomies that were resolved. From reading of the code, this would be trivial to do.
A newick string like this `(()A,(B,C));` is read by Dendropy as having tips labelled A,B, & C, not None,B,C. I.e. the terminating unnamed unification `()` before the A is being...
At https://pythonhosted.org/DendroPy/schemas/newick.html (which I presume is generated from the codebase), under reading, it says - suppress_internal_node_taxa (boolean, default: True) – If False, internal node labels will be instantantiated into Taxon...
I'd like to be able to specify my own line delimiter (could be just a single character). I have a 200Mb file with no newlines in it that I'd like...
With some OSes / libraries (but not all) I get the following message when running the attached .sites file (here saved as .txt to allow github uploading). ``` arg-sample --sites...
I think by default when running `sim_ancestry` we set `ts.tables.populations.metadata_schema` to something that requires a name and description. If I do a search in the docs for "schema", I can't...
Tthe pedigree simulation code seems not to produce "unary" nodes for the intermediate nodes in the tree sequence, so even if a lineage goes through a known node, this information...
It [looks to me](https://github.com/tskit-dev/msprime/issues/1734#issuecomment-861600728) as if the population_size and initial_size parameters are specified in number of individuals, not number of genomes. That is, they depend on the "ploidy" setting. For...
It's always bothered me that the `record_full_arg` output has 2 nodes that are only identifiable as grouped together because they are at the same time (unique in the nonWF case,...
For simplicity, code to check for consistency of the chromosome name was removed from the new [`msprime.read_hapmap()` code](https://github.com/tskit-dev/msprime/pull/1346). However, it seems a good idea to check, by default, that if...