I'd second the posts above, but can't resist plugging another option for actually plotting your data once you have selected the data you want to plot:

<shameless plug> Chart::Graph::Gnuplot </shameless plug>

In reply to Re: Ploting a 2d graph ...Bioinformatics by eXile
in thread Ploting a 2d graph ...Bioinformatics by govindkailas

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