Build instructions: javac -cp args4j-2.0.12.jar:src/main/java -d bin src/main/java/de/tum/in/lrr/hmm/cli/*.java ********** Testing: javac -cp args4j-2.0.12.jar:test/junit_3.8.2.v20080602-1318.jar:src/main/java:src/test/java -d test src/test/java/de/tum/in/lrr/hmm/AllTests.java java -cp args4j-2.0.12.jar:test/junit_3.8.2.v20080602-1318.jar:test junit.textui.TestRunner de.tum.in.lrr.hmm.AllTests ********** Runnning: java -cp args4j-2.0.12.jar:bin de.tum.in.lrr.hmm.cli.SequenceTrainer Print usage. java -cp args4j-2.0.12.jar:bin de.tum.in.lrr.hmm.cli.SequenceTrainer <options> <HMM output file> <sequence file(s)...> Creates a new model from the sequence files and writes it to the HMM output file. Sequence files can be either in EMBL or FASTA format. Example sequences files are example/hpv_e1.fasta, example/hpv_e1_test_full.embl, or example/hpv_e1_training.embl. java -cp args4j-2.0.12.jar:bin de.tum.in.lrr.hmm.cli.SequenceFinder Print usage. java -cp args4j-2.0.12.jar:bin de.tum.in.lrr.hmm.cli.SequenceFinder <options> <HMM file> <sequence file> Reads a model from the HMM file and looks for matching sequences in the sequence file. Useful Java VM options: -server start server VM (longer startup time, more optimizations) -ea enable assertions -Xmx1024m increase maximum Java heap size to 1GB (adjust as neccessary) -Xss2m increase Java stack size to 2MB