petermr
commented
9 years ago It needs about a morning for me to revise the correction of the taxa. It's not going to seriously affect the general structure of the tree. We are not creating the final result, but making sure the process works.
On Sun, Aug 30, 2015 at 10:15 PM, Ross Mounce notifications@github.com wrote:
I have just noticed that the binomial lookup correction isn't making it into the output Newick files.
There are lots of pairs of taxa, where one is obviously a mispelling variant in my MRP matrix file: Xylella_fastidinsa' & 'Xylella_fastidiosa' | 'Xylanimonas_cellulosilytica' & 'Xylanomonas_cellulosilytica' | 'Xanthophyllomyces_dendrolhous' & 'Xanthophyllomyces_dendrorhous' 'Xanthomonas_campeslris' & 'Xanthomonas_campestris'
I shall trace examples back to specific source tree files and see if it's correct in the NeXML. It needs to be correct in the Newick (nwk) too.
— Reply to this email directly or view it on GitHub https://github.com/ContentMine/phylotree/issues/54.
Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069
I have just noticed that the binomial lookup correction isn't making it into the output Newick files.
There are lots of pairs of taxa, where one is obviously a mispelling variant in my MRP matrix file: Xylella_fastidinsa' & 'Xylella_fastidiosa' | 'Xylanimonas_cellulosilytica' & 'Xylanomonas_cellulosilytica' | 'Xanthophyllomyces_dendrolhous' & 'Xanthophyllomyces_dendrorhous' 'Xanthomonas_campeslris' & 'Xanthomonas_campestris'
I shall trace examples back to specific source tree files and see if it's correct in the NeXML. It needs to be correct in the Newick (nwk) too.
Example trace: https://github.com/ContentMine/ijsem/blob/master/500D/ijs.0.2008_000836-0-000.pbm/results/phylotree/001.nexml.xml
<otu id="otu24" cmphy:edit="[0__O]" cmphy:genus="Xanthophyllomyces" cmphy:species="dendrolhous"
dendrolhous should be dendrorhous