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@SChamberlain Thought I might tap some of your `plyr`/`reshape2` awesomeness here:
`get_character_list` extracts a list of data.frames. Each data frame has taxon names as the rownames and characte…
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Does the current conversion to ape lose element id information? Can we program around this while still maintaining valid phylo objects?
E.g. once I have coerced a nexml file to a phylo tree and iden…
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Treebase import seems to be randomizing the names of the trees on import. For example http://www.reelab.net/phylografter/study/view/2044 has the wrong tree labels for the newick trees.
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Bio-Phylo-0.55 fails its tests when SVG.pm is installed with perl-5.18.0 from perlbrew on Mageia Linux Cauldron x86-64. Here is the shell session. Please look into fixing it.
``` text
shlomif@telaviv…
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A running list of questions that I might direct to Matt if I cannot figure them out:
- Can we get (public) endpoints/URLs to all the public EML files in KNB?
- How should we be generating `id` attribu…
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EMAIL REPORTED:
I have the need to import in ete2 a netwick tree perform decoration with several attributes and
then transform in nexml. Unfortunately the edge tag in nexml does not
have the compulso…
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There has to be a way to read in a phylogenetic tree coming from Phylografter and represented in Nexson (i.e. NeXML in JSON) format.
[Renamed issue, was "Nexson tree import]
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This character matrix was written by Mesquite:
https://gist.github.com/3208886
The following null pointer exception occurs when trying to read it using Mesquite:
Going to read matrix of type Standa…
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Hi Rutger,
1/
I was currently trying to debug some code I wrote that takes in a Newick tree, and I think I can trace my problem back to the fact that I had some nodes names containing a semicolon (o…
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When you load the below-linked NEXUS file into Mesquite and save as NeXML, polymorphic or uncertain states are turned into more states, rather than polymorphic or uncertain statesets, for example:
``…