msprime
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Simulate genealogical trees and genomic sequence data using population genetic models
For some applications it will be useful to condition on a specific ancestral sequence. This should basically be the same as the MatrixMutationModel, except it takes as first parameter the...
A fundamental part of the work in coalescent simulation is to keep track of the amount of ancestral material remaining for each interval along the genome. In msprime we currently...
this PR is dealing with issues #1762 and #1780. this implements a NeutralFixation model, which deals with a structured coalescent model akin to a selective sweep but for the case...
The firsts symptoms of the error in #1966 were a Jupyter notebook kernel repeatedly dying. This behavior is due to the use of `tsk_bug_assert` , which calls `abort`, preventing any...
Originally discussed in PR #1953: > I think the solution to this (for the next msprime?) is to include a `generation_time` argument that scales all the times, and would make...
Our analysis of the running time of Hudson's algorithm in the msprime 1.0 paper predicts that a lot of the time spent for long genomes will be in events that...
It would be very useful to be able to support pedigrees that have either no time associated, or partial time values. We avoided doing this in the initial implementation as...
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...
In #1858 we added the sim_pedigree function, which is a forwards-time WF simulator. It would be useful to be able to simulate pedigrees under different demographies, etc but implementing all...
This would allow us to exactly track where ancestral material passed through all individuals in the pedigree, which would be useful for explanatory purposes and also probably helpful for some...