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Proposal for HGT visualization:
Similar to the functionality of `node.add_face`, a new method will be added to the Tree instance to control de visualization of horizontal links between nodes (i.e. HG…
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Hello! I want to ask a question about the biological interpretation of horizontal gene transfer. I used MetaCHIP to get the genes that had a horizontal transfer between MAGs. The resulting genes are…
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Write a SLiM recipe in which the organism reproduces "like a virus", i.e.,
- asexually
- haploid
... and, later on...
- horizontal gene transfer (ie recombination)
This should also be in …
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Hi,
I'm curious if it is possible to modify the pseudo-Dollo model, from a global one where regains are possible on any branch to a local one where regains are only possible on branches connected…
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Dear Mr. Emms,
I am Matteo Brunialti, a student of bachelor degree of bioinformatics in Sapienza University of Rome, I am currently doing a thesis about horizontal gene transfer.
During the devel…
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These are just some thoughts, free to ignore if you've considered them already or if I'm misunderstanding how autometa does taxon assignments
If I understand it right, currently Autometa uses som…
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Is there a specific interpretation I should make if a gene is assigned to an orthogroup, but it does not appear it in a HOG? I've tried looking through the documentation, but I don't see much about HO…
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Hello, I'm trying to form protein clusters. These proteins may have diverged for a very long time as I am looking for horizontal gene transfer events. So I expect to observe only a few conserved doma…
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The bottom part of mathlib is quite a mess. Algebra, data structures and order theory *could* be developed separately (at least for a while) but are not. Instead, "horizontal" imports keep happening b…
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Motivation: I have colleagues who would like to use this tool, but for more than just generating taxonomic profiles. I would also like to utilize the resulting SAM files to do things like investigate …