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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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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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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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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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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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**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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### Current Behavior
```sh
$ augur refine --tree results/tree_raw.nwk --alignment results/aligned.fasta --metadata data/metadata.tsv --output-tree results/tree.nwk --output-node-data resu…
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The genic selection model is not giving the correct output when the starting frequency is high.
The code to reproduce the plot below is [here](https://github.com/molpopgen/msprime_discoal_compariso…
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[De Maio et al](http://virological.org/t/issues-with-sars-cov-2-sequencing-data/473) provide a number of candidates for masking from phylogentic reconstructions, grouped into a number of categories. W…