[Biojava-l] biojava3 getting the features from alignedsequence

[Hara Dilley]

Hi,

I would like to align a set of sequences against a scaffold and get the list of the modifications for each aligned sequence.
I am using biojava3
I have tried to create a profile  thinking that I can get the AlignedSequences from it but that it appears to be null.
Here is part of my code:

Profile<ProteinSequence, AminoAcidCompound> profile = Alignments.getMultipleSequenceAlignment(lst);
Profile.getAlignedSequence(0);

Can someone please point to an example for this or to the classes I have to use.
Thank you,
Hara