[Biojava-l] Problem with Multiple Sequence Alignment in BioJava

[udana chathuranga]

hi all,

When I was going through the biojava cookbook as I was interested in this
project. I tried the example in the page
http://biojava.org/wiki/BioJava:CookBook3:MSA and I got a classnotfound
exception for the line "Profile<ProteinSequence, AminoAcidCompound> profile
= Alignments.getMultipleSequenceAlignment(lst);".

Error Message:

Exception in thread "main" java.lang.NoClassDefFoundError:
org/forester/phylogenyinference/DistanceMatrix
    at
org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
    at CookbookMSA.multipleSequenceAlignment(CookbookMSA.java:29)
    at CookbookMSA.main(CookbookMSA.java:18)
Caused by: java.lang.ClassNotFoundException:
org.forester.phylogenyinference.DistanceMatrix
    at java.net.URLClassLoader$1.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClassInternal(Unknown Source)

Is this a know issue or Am I doing something wrong with the code?
Help me on this I have attached the java source file that I have tried.

Thanks
Regards
udana.
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