If your javaprg reads a sequence from the command line:

cat sequences | parallel javaprg --sequence {} > output
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If your javaprg reads a sequence from standard input (STDIN):

cat sequences | parallel --pipe -N1 javaprg > output
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If you sequences are delimited by \n> and javaprg wants 10 records per run:

cat sequences.fasta | parallel --recstart '>' --recend '\n' --pipe -N1
+0 javaprg > output
[download]

See also biostars.org/p/63816/