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I am aligning 5 assembled mammalian genomes, and the runtime is over 2 months at this point. It does not appear to have crashed, as the log file has lines from today. Is there any way to determine wh…
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We claim that tsinfer, not being particularly model-based, should be robust to selection. We can test this by carrying out a selective sweep and inferring + dating the result.
The plots below show …
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Dear Devs,
I hope that you are well.
I am using TreeTime (v 0.11.3), installed with `conda install bioconda::treetime`.
I am using the ancestral sequence reconstruction (with VCF files) comma…
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Starting to think about this in the context of generating a lot of 10x VDJ data... it seems we will want to (eventually) have a way for `Clone`s to contain `cell`s (see https://github.com/airr-communi…
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Hi,
Thank you for your tool.
I am more interested in mutability likelihood than the one computed by default after inferring the parameters of the galton branching process.
I tried to use the .p …
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- [X] 1) download sequences from Genbank (with possibility of addon to augment request specifications later); access problem? (https://www.ncbi.nlm.nih.gov/genbank/) (resolved by https://github.com/kr…
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Dear @ChrisHIV,
Could you please tell me where to find the data and code for Fig.2? Thanks.
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Hello. Pyjar appears to be causing a core dump. This may be related to this [issue](https://github.com/nickjcroucher/gubbins/issues/366). This was run on the cleaned output of Snippy from 104 _A. baum…
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(epik) genome@limsfep-zen-32c:/data/genome/run/snyoo/ipk$ python ipk.py build -w ./ \
> -r Tricholoma_ref_aln.fasta \
> -t Tricholoma_ref_aln.fasta.raxml.bestTree.rooted \
> -m GTR -a 0.42 -k 10 \
…
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**Submitting author:** @TahiriNadia (Nadia Tahiri)
**Repository:** https://github.com/tahiri-lab/aPhyloGeo
**Branch with paper.md** (empty if default branch): joss-journal
**Version:** v1.0.0
**Editor…