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Latest revision as of 12:52, 24 September 2009

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Core commits

Recent Commits to biopython:master

test_Prank_tool: find ".best.nex" output file from the latest Prank
test_Prank_tool: handle Prank's new stdout logging style
Prank wrapper: added versions to option docs for -(show|no)(xml|tree) change
NewickIO: parse branch lengths in scientific notation (Issue #220)
Only add an edge annotation/branch length if the clade specifies a branch length.
Use rdflib.URIRefs for URIs in yielded statements; if part of a statement is a string, treat it as raw RDF.
Use @base for more concise URLs.
CDAO trees and clades have a [(predicate,object)] `attributes` list containing any additional triples with that tree/clade as subject.
Write triples directly to file instead of going through rdflib. This avoids storing entire graph in memory.
Updating CDAO library to remove dependency on librdf. Using RDFlib instead.
Fix typo in class name (docstring change)
GenBank: Give better error output on invalid qualifiers
Phylo.draw: rename local variables for PEP8 compliance
Phylo.draw: edited docstring & made the printed error message a ValueError
Added changes based on feedback from @etal
Added linecollection for clade lines option
Kwargs are passed as pyplot options
Downgrade non-null SFF padding error to a warning (issue #219).
Merge branch 'master', remote-tracking branch 'origin'
Added -showxml and -showtree options to Prank wrapper
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