File list (Check if you may need any files):
CLParameters.java
DemoChart1.java
DemoChart2.java
FastaDivider.java
FileConverter.java
jwu
...\align
...\.....\Appear.java
...\.....\ColorRGB.java
...\.....\MultiSeqAlign.java
...\.....\Pattern.java
...\.....\Patterns.java
...\.....\Sequence.java
...\BarChartDemo1.java
...\bio
...\...\DNA.java
...\...\NA.java
...\...\Sequence.java
...\...\SequenceType.java
...\ExtensionFileFilter.java
...\gui
...\Jobs.java
...\JobsWithGroup.java
...\pattern
...\.......\Pattern.java
...\.......\Patterns.java
...\.......\PatternTree.java
...\.......\PatternTreeNode.java
...\.......\PVPair.java
...\.......\Score.java
...\SimpleTextEditor.java
...\SVGChart1.java
...\TopN.java
...\TopNold.java
MSAAppear.java
MSAColor.java
MSALocation.java
OnePassReading.java
PatternTest.java
RegexTester.java
SequenceGenerator.java
Test.java
TestTree.java
TreeMapTester.java