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Recent Commits to biopython:master PDB: copy the .xtra dictionary in Atom (Bug #3358) fix ignored exception in test_PAML_tools by removing unnecessary cleanup code add PAML codeml test case for single NSsite cases fix new bug in PAML parsing of models with >1 NSsites fix bug in PAML codeml parsing of site-class model names Brandon has contributed to the current release (PAML mult-genes) fix errors during PAML test cleanup add PAML codeml parsing for results with multiple genes add tests for PAML codeml results with multiple genes Phylo: added outgroup_branch_length argument to root_with_outgroup Tweak BLASTP test to cope with BLAST 2.2.26+ output Add Bow and John to NEWS file for NCBI BLAST 2.2.26+ plain text, Issue #3346 updated: NCBIStandalone parser for handling 2.2.26+ blasts (incorporting fix from John Comeau Argument -max_hsps_per_subject is new in BLAST 2.2.26+ added: max_hsps_per_subject option for BLAST+ wrapper Remove some Python 2.4 specific code in Bio.Application Fix a small error in the previous patch Fixing Entity copy method to preserve child ordering. Fix tutorial typo reported by Partrick P, closes Issue 3348 PDB: Added a get_residues() method to the Chain class