The module highlightMSA contains a class called hMSA that hold a multiple sequence alignment read by AlignIO of BioPython and regions along these sequences can be painted in two colors (for now). The coloring is according to the name of the sequence in the MSA file (I like to use TXID as the name) and the range of nucleotides. The other method in the module print this MSA to an RTF file (you will need PyRTF from http://pyrtf.sourceforge.net/) with the backgrounds of the regions colored in different colors.