[Biojava-l] Alignmente algorithms implemented by BioJava

Hi, Can somebody tell me what algorithms Biojava uses to make local alignments and multiples alignments? I'm Serching it on the Documentation but I have not found it? Where could I find it? I'm working on a Java Environment for Analysis and Alignment of Sequences! Thanks, Anderson Moura - B

Re: [Biojava-l] Alignmente algorithms implemented by BioJava

Hi there, The CVS code in BioJava contains the necessary classes to perform both Smith-Waterman and Needleman-Wunch pairwise alignments. Just have a look at the Javadocs for instructions. The preferred way around here is based around using HMMs to perform the alignments; for this look at the Cookb

RES: [Biojava-l] Alignmente algorithms implemented by BioJava

Thanks, I was really looking for these 3 ones!! I'm very knew in Bioinformatics, so can I ask if there is others algorithms that are really used? I only know these 3 ones (SW, NW and HMM)!! Thanks Anderson Moura - Brazil -Mensagem original- De: Sylvain Foisy [mailto:[EMAIL PROTECTED] En

Re: [Biojava-l] Alignmente algorithms implemented by BioJava

Anderson Moura da Silva escreveu: Hi, Can somebody tell me what algorithms Biojava uses to make local alignments and multiples alignments? I'm Serching it on the Documentation but I have not found it? Where could I find it? I'm working on a Java Environment for Analysis and Alignment of Sequ