Protocol Online logo
Top : New Forum Archives (2009-): : Bioinformatics and Biostatistics

Fragment analysis software for linux - (Jun/24/2013 )


I haven't been able to find a program that reads .fsa files and runs natively under linux. Currently I'm using PeakScanner in Virtualbox, which isn't ideal. I would appreciate if someone could point me to an appropriate program, preferably a free one.



not sure what you want to analyse (don't know peakscanner), but software based on java should do the job?


How about Traceviewer (I haven't used it but it is win, linux and mac supported).


What I need is to score microsatellite (and AFLP) markers (i.e. I need to look at a .fsa chromatogram to check out the quality of the peaks and assign fragment lengths).

I haven't been able to find anything in java or in R. Traceviewer is for DNA sequences, not fragments.


I found this for R: (PDF)

Also: http://sourceforge.n...ts/genographer/