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Hello,
Thank you for the easy to use tools and great documentation. I have a question about one of the rules in the main Snakemake file. In the message it says "not inferring ambiguous mutations", …
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Hello,
I am having an issue plotting the GADMA results. Mainly, the divergence times are pretty far off where I expected them to be. I am not 100% sure that I am doing it correctly, so I have expla…
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Currently, we're counting any mutation different from the nearest sequence as a new mutation.
This doesn't correctly handle the case where the mutation happened on the nearest sequence instead of o…
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Dear Dr.@MichaelHiller,
Thank you!
I have modified these scripts and ran successfully. To ensure that I properly ran these scripts, I tried to replicate the results of the `Loss of Vitamin C Synth…
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The newick format will output a single tree. There is a "standard" format for *sets* of trees, which is NEXUS. I have code for writing a tree sequence out to nexus, which is fairly simply, but require…
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I think it shouldn't be too hard to allow samples with missing data, ~~presumably marked as a variant whose allelic state is set to `tskit.NULL`~~ using the current notation this would be an allelic s…
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**[Original report](https://bitbucket.org/simongravel/moments//issues/6) by Ethan Gyllenhaal (Bitbucket: [ethanfgyllenhaal](https://bitbucket.org/ethanfgyllenhaal), ).**
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See #442.
This is probably expected for time-scaled discrete-generation simulations, but we should satisfy ourselves that there isn't another underlying problem here. And is this problematic in gen…
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We are potentially using too many back mutations when placing non-inference sites. We should try to find clades of ancestral state samples and put mutations over those rather than just putting a back …
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the new Generic model classes that were created in `stdpopsim` give us the opportunity to test how well things should work under a variety of very simple models. Below I have results from simulated hu…