NCBItools programs like blastall are deprecated and replaced by a new blast+ suite of programs. BioPython is supporting these new programs. The use of NCBIStandalone methods in SequenceSearcher needs to be replaced.
See: BioPython tutorial
Example: (not tested) see commented-out code in SequenceSearcher.localPsiBlast
(1) replace installation instructions on biskit.sf.net to switch users to blast+
(2) replace all calls to blastall and blastpgp
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