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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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Hi!
I am trying to reconstruct a sequence for every node in the tree. I have been following the manual the best I could and I only get 1 sequence as an output when parsing it out. I use this inside…
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Hi!
I have a single dataset, and I used it as input in (1) timetree construction, (2) ancestral sequence reconstruction, and (3) mugration analysis. My doubt is why each tree looks very different.…
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I am trying to use ancestral sequence reconstruction in IQ-TREE (version 2.2.2.7 COVID-edition for Mac OS X 64-bit built May 30 2023) on fixed trees with non-reversible Lie Markov models. I am using t…
brj1 updated
8 months ago
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Hi, I encounter the same problem as in https://github.com/facebookresearch/LAMA/issues/10.
And I found the reason why 2 examples are filtered is that the `obj_label` are `1970s` and `1990s`. And in `…
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Hello,
I have 206 sequences whose whole genome alignment is about 653 Mb. The run has been staying at joint ancestral reconstruction step for a day now. I'm wondering whether it is stalled or how l…
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Hi there!
I am testing out BUSTED on an alignment and I got an error which I cannot find anyone else running into online. This same error happened for 2 different alignments I tried to run. I thin…
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Dear Professor,
I would like to ask whether "Forwardgenomics" is suitable for the analysis of CNE differences in new phenotypic species.
I wish all the best!