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The current documentation for `augur ancestral` (augur v10) makes it clear that ambiguous sites are not reconstructed by default:
```
--keep-ambiguous do not infer nucleotides at ambiguous …
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Hi everyone,
I am trying to make an SFS using ANGSD but got a bit confused by the ancestral state.
My case is ddRAdSeq pair-end reads of a fish. Samples are generated as fq.gz for read1 and rea…
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Hi, I used the lc.loter_smooth to get the result. But the result is the classification of each single SNPs. How I can get the introgressed regions? By merging the consecutive SNPs belong to a same sou…
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(Continuing on the discussion from #273 ), currently if we provide either the `mismatch_rate` or the `recombination_rate` parameter to match_samples or match_ancestors, it is expected to be an array o…
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Once the dust settles, we'll want to add more complexity. :P
Currently, demes deals with **concrete** demographic models, ie. those with fixed parameter values. It would be really neat if we could …
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In several cases we want to [union](https://github.com/tskit-dev/tskit/pull/623) some inferred tree sequences together. For example, we might have matched UK-Biobank against an ancestors tree sequence…
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Hi,
I found a small bug in the tutorial on https://nextstrain.org/docs/tutorials/tb, because it throws an error with the output definition.
I think, instead of:
```
augur ancestral \
--tr…
arpoe updated
4 years ago
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The idea is simple to implement and well-scoped as part of TF Distributions. I personally like the idea of even having it be the default for Gamma, Beta, and others. The gradient implementations may b…
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When we use the tree sequence as inferred using the most recent tsinfer version as an ancestors TS, using `tsutil`'s [combine-ukbb-1kg](https://github.com/mcveanlab/treeseq-inference/blob/0cbbb062c96a…
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_Note: this bug has been fixed. The issue is described here for posterity._
The Arabidopsis species definition uses `recombination_rate=8.1e-9`. Above the species definition is the following commen…