I have a web-based tool for plotting graphs (in the sense of 'graph theory' graphs) called NETPLOT
This is a perl script for plotting square matrices. Input is a table, output is a heat-map .PNG file (i.e. 'warm' colours represent higher numbers in the input table)
I have a somewhat scruffy set of PERL and C++ programs to calculate and display UPGMA trees. Basically this involves taking a series of entities, calculating pairwise similarity scores for every pair and then constructing a tree from them.
maketree - for creating trees with UPGMA using distance matrices (C++)
plotTree - for visualising trees from maketree as .PNGs (Perl) (N.B. Requires GD library)
I have a PERL script that takes RF and %T values and calculates and plots (to a postscript file and/or GnuPlot data and instruction files) a Ferguson plot and the resulting Kr vs. MW plot. Takes standards and unknowns.
Takes a tab-separated table (col 1: sample name, col 2: OD280, col3: absorbance of 1mg/ml protein) and given the volume capable of being loaded in a lane on a gel and a desired protein amount, outputs what should be mixed in what ratios and what resulting concentration will be given.
calcGel
Let me know if you use these and if you have any improvements / suggestions...