msprime
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tskit-dev
Simulate genealogical trees and genomic sequence data using population genetic models
The general idea of how this should be done is already incorporated in `algorithms.py`, what's left is implementing this in C and adding a fair amount of tests.
This PR will add an option (`--ce-from-nwk`) to provide a tree in newick format that will be respected during simulation (hudson model). The aim is to make sure that the...
I just followed what's done in [ancestry.py](https://github.com/tskit-dev/msprime/blob/main/msprime/ancestry.py#L573) here.
The following code has per-bp resolution on the RateMap: ``` L = 1e5 ts = msprime.sim_ancestry(1000, sequence_length=L, recombination_rate=1e-8, population_size=1e4) rm = msprime.RateMap( position=np.linspace(0, L, int(L+1)), rate=rng.exponential(size=int(L))*1e-8 ) mts = msprime.sim_mutations(ts,...
In particular, that the exact transition is determined once a mutation has been laid down (so that the rate is the sum of all the possible mutation rates at that...
Dear all, I was checking variable implementations of the (joint) allele frequency spectrum folding and went through the [polarisation subsection](https://tskit.dev/tskit/docs/stable/stats.html#polarisation) in `msprime`. I am not sure I clearly understood the...
Getting this error when I run on ARM mac in upstream CI: ``` Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/msprime/__init__.py:28: in 27 from msprime._msprime import ( 28 E ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/msprime/_msprime.cpython-311-darwin.so, 0x0002): symbol not found in flat...