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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-…
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Tthe pedigree simulation code seems not to produce "unary" nodes for the intermediate nodes in the tree sequence, so even if a lineage goes through a known node, this information is lost. For instance…
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This is false. BEAST offers many other tree priors, many of which are more appropriate than Yule (e.g. BD contemp)
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Hello,
I hope all is well! We have been very interested in using phylonco, specifically the binary substitution model and error model. We have first simulated data with a known mutation rate and …
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Hi ~
I want use Phybase to simulate gene trees (Species tree constructed by Astral), and some articles said it should phased all the terminal tips with a branch length equal to 1. Is there necessary…
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I've been trying to run a coalescent simulation using a standard model from the library - but instead of the default Hudson model, I want the simulation to use the discrete-time-Wright-Fisher model fo…
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I'm just wondering if you might think about outputting the tcPBWT in tree sequence format (also for output from https://github.com/nvalimak/argentum)? There might be problems with cyclical structures …
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Hello, Professor,
I am installing the astral-mp, my command is :
git clone https://github.com/smirarab/ASTRAL/
cd ASTRAL
git checkout MP
./make.sh
java -D"java.library.path=/data/01/user157/sof…
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**Authors:** Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn, Luay Nakhleh
**Source code:** https://bioinfocs.rice.edu/software/phmm
**License:** GNU GPLv3
**Abstract:**
One …
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Hi, Yun
Here is the following question. With the vcf from #14, SINGER cannot work. Do you know why?
```bash
Number of incompatibilities: 687
Number of flippings: 23
Iteration: 53
[18:50:50.0…
baozg updated
1 month ago