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Hi @schultzm, this looks like a very useful tool and thank you for bringing this out. Do you know if this would also work for resolving polytomies in IQ-TREE or RAxML output files? From my quick testi…
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Hi!
Thanks a lot for developing this useful tool! I am currently trying to run it on a set of ~2,000 viral genomes.
I followed the GitHub instructions and:
- I also added prodigal to the path (…
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## Expected Behavior
Using python code below, I tried to open nw file generated with ' foldmason easy-msa'
`from ete3 import Tree`
`tree = Tree("/Users/xx/Documents/xx_project/Rotation1/Patho/xx/M…
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I ran orthofinder with -msa in hopes that it would add support values to gene trees. And it kind of has. In that some trees have them and some don't. As an example, here are two trees from the same ru…
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Is it possible to programmatically export order of taxa on the left and right of a tanglegram. I assumed that "Export -> Taxon Display Labels..." would do it, but the ~legalese~labels seem not to be …
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It would be cool to be able to import a Newick tree (with or without node ages) to form a base `Deme` object that can then be annotated with other details (split times, population sizes, etc).
Simi…
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Support for the [Newick format](https://en.wikipedia.org/wiki/Newick_format) in imports and exports seems a useful thing to do, especially for phylogenetic data.
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Check newick format, alert user if input is invalid.
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Here is an explanation of the Newick Tree File Format - http://evolution.genetics.washington.edu/phylip/newicktree.html
Reading and writing in this format is going to be a bottleneck in large datas…
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Do you, or would you, support reading graphs specified in a Newick format? https://en.wikipedia.org/wiki/Newick_format ? Perhaps in the context of MetaGraphs (as the Newick format contains some metada…