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Hi @tgvaughan ,
Is there a way to extract the time when each leaf (tip) in the output tree was actually sampled during the simulation e.g. from a punctualReaction below:
` I -> sample `
I would lik…
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## The problem
TreeTime has currently a very rudimentary way of resolving polytomies (multi-furcations in the tree).
When this was initially put in place it was never meant to resolve large polyt…
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For tree sequences inferred from simulations, we can't directly compare inferred dates to true dates because node sets differ between the inference and the simulation.
Instead, we've been looking …
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augur refine -t indian_837_data.nwk -a aligned_indian_837.fasta --metadata metadata_2020-06-16_07-16.tsv --output-tree refine_indian_837_data.nwk --output-node-data branch_lengths_indian_837.json --ro…
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Hello,
I am facing errors using mp-est 2.0, both at the compilation step and also if I opt to use the provided binary.
My computer runs macOS Sierra 10.12.6 and the following are my steps for re…
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Alister and Edmon should identify an appropriate workshop or a mid-key conference where we could write up and present the results. I do not think we have material for anything ambitious, but it would …
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### Author(s) of proposal
Ran Wei
### Name of taxon
Lepisorus
### Rank of taxon
Genus
### Approximate number of species affected
_No response_
### Description of change
Lump…
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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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**Short description of the problem:**
Simulation with OutOfAfrica_3G09 model generates two haplotypes with a very high amount of shared derived sites causing the diploid individuals constructed b…
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Hi Dr. Deng,
Could you also upload the data for biasgenes_inf