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I am running checkM tree and tree_qa to obtain an idea of the taxa insertion high of my bins. But, when I run the commands all works and generate files that I cannot use in any tree rendering software…
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**Submitting author:** @alex2cris (alexis criscuolo)
**Repository:** https://gitlab.pasteur.fr/GIPhy/REQ
**Version:** v1.2.180713ac
**Editor:** @jedbrown
**Reviewer:** Pending
**Author instructions**…
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Hello,
I am trying to simulate gene trees from a fixed species tree that is very large (10k leaves). I passed the tree in Newick format via the -S option but got the error "Argument list too long". I…
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When output.format is any of the following
`"newick.all", "newick.sdm", "newick.median", "phylo.sdm", "phylo.median", "phylo.median", "phylo.all", "html", "data.frame"`
The output should show a …
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Current Capabilities:
* "Import" - Opens a file of some format which adds data to the analysis.
* "Export" - Saves some portion of the analysis as the appropriate format (Image, Fasta, Newick, etc.)…
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The line numbers in the (full) names of the instances do not account for comments ('#').
e.g. access-argument/ratings(10,37) is actually in line 29 in als.physl (line number says it should be at line…
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this is what I try to do:
http://merenlab.org/2016/02/27/the-anvio-interactive-interface/#11-newick-tree
And this is the error I get:
```
anvi-interactive --manual -t semi-core-phylogeny.newick …
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The reason is apparently a bracket in some character name, but I don't know how it should actually find any brackets, given that glottolog names don't have them?
Here's my traceback when trying to ge…
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Some questions about the files available for download from Glottolog & WALS. I wanted to derive the name of the top-genetic unit and WALS-genus for as many Glottolog languages as possible. So, Siva an…
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This is meant to be a sketch of an idea how we could visualize the evaluation of an execution tree. Let's assume we have a simple expression `store(A, add(B, C))`, then the following visualization all…