There are 2 repositories under java-bioinformatics topic.
ALignment Transformation EnviRonment
bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatics pipeline able to perform a full DNA methylation level analysis
BLAST DataBase Manager
LA-iMageS: a software for elemental distribution bioimaging using LA-ICP-MS data
Automatic Detection of Positively Selected Sites