Package edu.cornell.med.alignments

Provides utilities for parsing and writing alignment files.

See:
          Description

Interface Summary
AlignmentParser Reads an alignment and converts it into a BiologicalAlignment.
AlignmentWriter Writes a BiologicalAlignment.
 

Class Summary
AlignmentConservation Takes in an alignment in ClustalW format, parses it into a BiologicalAlignment, and calculates at each position whether the alignment reaches a user-specified conservation cutoff value.
ClustalwParser Takes in an alignment in ClustalW format, parses it into a BiologicalAlignment, and calculates at each position whether the alignment reaches a user-specified conservation cutoff value.
ClustalwWriter Writes a BiologicalAlignment in ClustalW format.
 

Package edu.cornell.med.alignments Description

Provides utilities for parsing and writing alignment files. Also provides functionality to calculate conservation at all positions in an alignment, according to user-defined criteria.

Package Specification

Related Documentation



Copyright © 2007 Institute for Computational Biomedicine, All Rights Reserved.