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smirarab / binning

Code for statistical binning and related scripts
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GARLI input trees #3

Open isgilman opened 7 years ago

isgilman commented 7 years ago

I'm currently trying to use trees generated in GARLI but they aren't being parsed correctly by DendroPy. This seems to me like it could be a quick fix, either by converting them into a form that looks like the output of RAxML, or by tweaking some of the code in 'remove_edges_from_tree.py` script. Do you have any suggestions for how to deal with this issue? I've attached an example of an output file from GARLI for reference.

Best, Ian

ML.best.tre.txt

smirarab commented 7 years ago

This seems like a nexus tree. You can use any number of existing tools to convey to newick. On Tue, Mar 14, 2017 at 7:07 PM Ian Gilman notifications@github.com wrote:

I'm currently trying to use trees generated in GARLI but they aren't being parsed correctly by DendroPy. This seems to me like it could be a quick fix, either by converting them into a form that looks like the output of RAxML, or by tweaking some of the code in 'remove_edges_from_tree.py` script. Do you have any suggestions for how to deal with this issue? I've attached an example of an output file from GARLI for reference.

Best, Ian

ML.best.tre.txt https://github.com/smirarab/binning/files/843218/ML.best.tre.txt

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