DO NOT FORK! This repository is outdated. It is only kept as a reference for old forks. Create a clean clone from https://github.com/biojava/biojava
Home Page: http://biojava.org/
License: Other
One output option at PFAM is usage of small caps to indicate non-conserved residues in multiple seq alignments. Trying to read such a file using BioJava results in an exception. It should be possible to read such files and treat small caps as normal AminoAcidCompound, leaving its interpretation to the user
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