[Biojava-dev] Alignment

[Kalle Näslund]

Ulisses Dias wrote:

>Hi All, 
>   I'd like to align two sequences and i want to know if there is a predefined function in biojava or I must to create one. If somebody could help me, I would be glad too.
> 
>Ulisses Dias
>
>	
>
Biojava doesnt have very fancy Alignment support, but there are some 
classes to help you read in a few formats. I tend to use the class 
org.biojava.bio.seq.io.MSFAlignmentFormat to read in alignments in MSF 
format or org.biojava.bio.seq.io.FastaAlignmentFormat for FASTA format. 
They will both give you back an Alignment that you then can use.

/Kalle