BLAST dot matrix output from command line

Question

[Nick]

Is there a way to generate the dot matrix output available on the online version of BLAST between two sequences from the command line?

[GenoMax]

If you are asking about dotplots then one of the options here should work: http://emboss.sourceforge.net/apps/cvs/emboss/apps/alignment_dot_plots_group.html

Answer 1

[shelkmike]

I've made a tool for this purpose, see https://github.com/shelkmike/Dot_plot_like_in_BLAST