[Biopython] help with confidence values on PhyloXML tree objects?
Jon Sanders
jsanders at oeb.harvard.edu
Fri Dec 9 21:53:12 UTC 2011
So I have two problems.
Problem 1: when importing my newick-formatted trees, which were generated
in PyCogent, the terminal labels and branch labels are read in as
confidence values because they're numerical. So
((((41:0.01494,44:0.00014)0.604:0...
is read in with blank name='' values and 41, 44, 0.605, etc. as
'confidence' values.
Problem 2: I would like to store multiple confidence values per node, but I
can't figure out how to do it.
I can get the plain old 'confidence' attribute set by:
clade.confidence = .05
but can't figure out how to add and set new confidence types. Any
suggestions?
Much appreciated,
-jon
--
"If you hold a cat by the tail you learn things you cannot learn any other
way."
--Mark Twain
More information about the Biopython
mailing list