Feature requests and bug reports should be added as Github issues. We welcome all feature requests, both large and small.

Some example feature requests:

• Balibase [#119]
• UniProt (XML/txt)
• port the BioJava 1 Chromatogram parser to BioJava 3 [#120]
• Variation APIs that bring together Ensembl Variation, VCF file format, GFF3+GVF file format, samtools, Picard, GATK, etc. [#121]
• SCOP2 parser [#82]

There are also a number of algorithms where we would be interested in Java ports.

You can also take a look at the current list of BioJava Modules and suggest other missing features.