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jjmccollum / teiphy

A Python package for converting TEI XML collations to NEXUS, BEAST 2.7 XML, and other formats
MIT License
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example with fewer witnesses and add into paper #40

Closed rbturnbull closed 2 years ago

jjmccollum commented 2 years ago

@rbturnbull Here's a 50% majority consensus tree I produced for the reduced collation (< 40 witnesses) in PAUP*:

ubs_ephesians_majority_consensus.pdf

The NEXUS file was generated from the TEI XML collation using the command

poetry run teiphy -t reconstructed -t defective -t orthographic -m overlap -m lac -s"*" -s T --states-present --fill-correctors example/ubs_ephesians.xml example.nexus

If this looks good, I can try to do the same with TNT or other software, if you'd like; just let me know.

rbturnbull commented 2 years ago

That looks great. Can you please save the consensus file in Newick format. We can style the tree a bit better for the paper. Let's try the same analysis with TNT and iqtree then I think we're good to go.

jjmccollum commented 2 years ago

Sure! I just sent you an e-mail with these files. TNT doesn't seem to offer an export direct to Newick format, although its "parenthetical" format looks essentially like Newick (except that it inconveniently uses the taxon indices instead of their labels).

jjmccollum commented 2 years ago

@rbturnbull Just for reference, here is the Newick format output from STEMMA:

('UBS':0, ((('TheodoreOfMopsuestia':2, ('63% 06C2':5, ('1505':0, '52% 1175':6, '2495':1, (('88':1, ('915':3, '32% 1881':6):2):4, ('606':1, '1910':4):1):1):1, '1611':1, 'syrp':6, 'syrhmg':0, ('syrh':1, ('18':1, '424':1, 'Chrysostom':2):2):1):3):3, (('vg':1, 'Pelagius':2):1, ((('06':0, '06C1':2, '37% 06C2':5):6, '010':1):2, ('Ambrosiaster':2, 'MariusVictorinus':2):6):6):4):3, ('02':5, ('copsa':6, 'copbo':1):5):2):2, (('33':4, ('P46':5, ('03':0, '48% 1175':6):6):6):2, ('Jerome':4, ('01':6, ('424C':3, ('1739':1, '68% 1881':6):2):3):2):1):2):0;
jjmccollum commented 2 years ago

@rbturnbull I just looked over the draft PDF of the paper to make some minor revisions, and the IQTREE plot looks really nice! Will that one be enough to include, or did you want to include results from other software, as well?

rbturnbull commented 2 years ago

I now think we just include one visualisation and include visualisations for the other packages in the documentation for the example file. What do you think?

jjmccollum commented 2 years ago

That makes sense to me. I just e-mailed you the tree files generated by MrBayes, in case you'd like to add them to the documentation for the MrBayes example. I also updated the example documentation to reflect how I ran the analysis on MrBayes and generated the files.

rbturnbull commented 2 years ago

i've just added in a max clade credibility tree from mrbayes. I think that page is all good now.