Hi bio-mailinglists, <br><br>does anyone here know of a tool or a library to display two (or more) sequences at the same time with coloured features? Possibly with lines, connecting some features from one sequence to the other (synteny-plot) ?
<br>Or to display two multiple alignments, one on top of each other, with colored features added?<br><br>It's not that it would be difficult to write, but programming visualisation usually takes a lot of time.<br>Bio::Graphics seems mainly concerned with one main sequence and features on it. Well, I could copy together two of these gif-images, but then there would be no connecting lines. Same applies for the graphics in Biojava or the gff2ps tool or all the multiple alignment viewers that I know (Bioedit, ClustalX). There is something called Toucan in Java, which displays at least several lines of gff-style-features, but no visible sequences and more importantly, no connecting lines. A recent software, Djinn lite, is using a similar kind of visualization to compare different spliced genes from various species, but it's mainly aimed at splicing and written in Visual Basic.
<br>I guess a good compromise might be the 3D viewer Sockeye, but I haven't seen any synteny-lines in sockeye yet.<br><br>I guess I must have missed something here. I cannot be the first one that would like to compare, say, two gff files, or two multiple alignments?
<br><br>Thanks a lot for any idea,<br>Max<br>