<div dir="ltr">Hi Alessandro,<div><br></div><div>Nobody ever claimed that BioJava is doing the same as Clustal. Not sure why you would expect that it would?</div><div><br></div><div>BioJava is a free project and nobody gets paid for working on it. If you find the documentation lacking, it would be great if you could contribute yourself. Considering the size of the project, we definitely could need help from more volunteers! </div><div><br></div><div>We are working on a new tutorial on github. That should make it easy for everybody to add or modify. In particular the chapter on alignment is only a placeholder at this stage. Any pull request with improved documentation will be welcome.</div><div><br></div><div><a href="https://github.com/biojava/biojava-tutorial">https://github.com/biojava/biojava-tutorial</a><br></div><div><br></div><div>Andreas</div><div><br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jun 16, 2015 at 7:53 PM, ALESSANDRO AIEZZA (RIT Student) <span dir="ltr"><<a href="mailto:axa9070@rit.edu" target="_blank">axa9070@rit.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">I've been followig this dev for a long time waiting patiently for someone to <b>finally</b> realize that BioJava produces nothing like clustal in MSAs. It's pretty disappointing.<div><br></div><div>Also, that cookbook could probably use some work. It's struggling.<div><div class="h5"><br><br>On Tuesday, June 16, 2015, stefan harjes <<a href="mailto:stefanharjes@yahoo.de" target="_blank">stefanharjes@yahoo.de</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><div style="color:rgb(0,0,0);font-family:HelveticaNeue,'Helvetica Neue',Helvetica,Arial,'Lucida Grande',sans-serif;font-size:16px;background-color:rgb(255,255,255)"><div>Hi biojava,</div><div><br></div><div dir="ltr">I am fighting with the multiple alignment of several DNASequences. When I use the biojava computation I get alignments errors regarding the gaps. Clustalx computes a much better result in comparison:</div><div dir="ltr"><br></div><div dir="ltr">biojava<br></div><div dir="ltr">TTGGGGCCTCTAAACGGGGTCTT<br>TTGGGGC-TCTAAC--GGGTCTT<br>TTGGGGCCTCTAAACGGG-TCTT<br><br>clustal<br>TTGGGGCCTCTAAACGGGGTCTT<br>TTGGGG-CTCT-AACGGG-TCTT<br>TTGGGGCCTCTAAACGGG-TCTT<br>****** **** ****<br></div><div>The most important difference is the second gap in the middle sequence, which is obviously better aligned in clustal. Any hints as to how to improve the biojava parameters/algorithms? <br></div><div><br></div><div>Cheers</div><div>Stefan</div><div>p.s.<br></div><div dir="ltr">I already tried to implement the actual gapPenalty which clustal uses which is 10/.1 for the pairwise and 10/.2 for the multiple alignment. (i.e. I changed all java short types to int, scaled all scoring parameters including the matrix by 10 and implemented two different gapPenalties in the two alignments). Unfortunately this does not change anything. <br></div><div dir="ltr">Does any of you guys have a copy of the IUB scoring matrix? which would be my next try?</div><div dir="ltr"><br></div><div dir="ltr"> <br></div></div></div></blockquote></div></div></div>
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