Hi there, you can use Image J. You may find several tutorial via google to learn how to do it under this envirnoment.

cheers

What would be the application? Are you interested in scoring bands as molecular markers to build a presence/absence matrix and then a dendrogram? If so, you can check this related question: https://www.researchgate.net/post/Gel_Image_banding_pattern_analysis_by_Dendrogram

My response then was the following, in case that is what you are looking for:

You could try PyElph, it's a freeware intended for automatic analysis of gel images. It computes distances between samples based on pattern similarities and generates the corresponding phylogenetic tree. It's quite friendly... give it a try! You can find the paper and link for downloading here: http://www.biomedcentral.com/1471-2105/13/9

Like Dr. Gustavo, my point is also - Are you interested in scoring matrix and then a dendrogram? Then you can go for NTSys-PC.

@ Guastavo and Kaushik the issue is primarily I am well versed with manual scoring, creation of dendrograms using both UPGMA and Bayesian matrix,but my querry in this particular case is I am searching for apackage which can do autmatic scoring of the fragments.I have got some names while going through net like Bandleader and gelquest but none of them are giving me 0,1 binary matrix.To both of you, my querry is this : :is there any software package available which will do the scoring , generate the 0.1 binary matrix which can then be used either in POPGENE or NTSYS?

Using PyElph, at the step "Band matching" there is a button "Export", you can use it to export the binary matrix as a text file if you want to generate the tree using another software.

Time ago I used GelQuant and it was also able to generate the binary matrix. Unfortunately it is not free, you can get it through Invitrogen.

Good luck!

thanks sir. I think the problem is solved with the PyElph.Its a great software.Thanks a lot

Really, PyElph is a good software indeed. I have done manual scoring and then with this software package. It worked efficiently. Moreover, the you can analysis your data and build dendrogram just like NTsys pc and all. Best of luck @Paromik.

You can try GelJ: http://gelj.sourceforge.net/