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Simulate genealogical trees and genomic sequence data using population genetic models
Implement inversions following the ARG model of http://www.nature.com/hdy/journal/v111/n3/full/hdy201338a.html Should be done at the same time as #11.
``` import tskit import msprime import random random.seed(6) nreps = 20 ne = [10, 1e2, 1e3, 1e4, 3e4, 5e4, 7e4, 1e5] for i in range(nreps): ifile = "slim_msp_rep_" + str(i+1)...
Should we provide an easy way to allocate names for the individuals generated in a SampleSet? E.g. ``` samples = [ msprime.SampleSet(["Ada", "Bob", "Cat"], population="pop_1", ploidy=2, time=0), ] ``` Or,...
Hello, I am simulating STRs, and I've encountered instances where I'm obtaining sites with more than nine allelic states, which isn't supported by the VCF file format. Consequently, I'm considering...
We don't see the version of msprime that the docs are for any more - something has change in the JupyterBook config. This may be an issue with the upstream...
Currently we say that Python 3.7+ is required, but we're now on Python 3.8+. We should be able to define a replacement macro for ``min_python_version`` in the docs config yaml,...
I'm using Windows laptop, and I can install msprime on my computer by using `conda`, but I cannot install msprime by using `pip`, as the following message shows up: `ERROR:...
Hi, I'm having issues converting my Demes graphs to msprime `Demography` objects; both population sizes and migration rates are missing unexpectedly. My Demes graphs match what I think I'm trying...
A natural addition to being able to keep a record of all genomes that we simulate through (i.e. keeping unary #2128 ) is to keep a record of the nodes...