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As far as I can see the only way to set up a binary ctmc or covarion analysis in BEAUTi is to use the included templates. This makes it hard to use a different template (e.g. MultiTypeTree or somethin…
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Hi Sir,
Thank you very much for this package!
I recently bumped into a difficulty in gene tree simulation using Phybase.
It failed to simulate gene trees for the third tree in the file but it …
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Hello:
Now that Skyfish is digesting my data and yielding Skyfish flavored Skylines of Ne and trees, I am turning to check convergence and estimates of parameters.
But the 'log' file with all the …
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In https://github.com/tskit-dev/tskit/pull/2381 @petrelharp pointed out that there are potentially 2 different ways of simplifying while keeping nodes which are partially coalescent and partially unar…
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Maki-defined Services should be independent of a centralized host or authority.
See also gordonwritescode/cointract.me#41 and martindale/shipright#17.
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Hi,
What is the unit of differentiation time (DivTime) between outgroup and target group? Like -DivTime 12.5 means that the differentiation time is 125,000 years ago? Thanks
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I've left a space in the docs (four paragraphs down at https://tskit.dev/tsdate/docs/latest/popsize.html) to place a population-size-over-time plot. I think this will involve plotting the IICR over ti…
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Hi Isaac,
I am having an issue about bootstrapping in fastsimcoal2 and appears that my point estimates fall outside 95% confidence intervals.
I have tried non-parametric bootstrapping by sampli…
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-How does mutation affect coalescence and finding the parent allele?
-How does convergent and divergent evolution play a role in temporal dynamics at discovering the parent allele, and the size of th…
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I gather from the T2T papers that the short arms of the acrocentric chromosomes (e.g. 13 & 14) exchange material e.g. through gene conversion (and maybe even recombination). This would be a neat test-…