Update README.md

README.md

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 Two scripts to isolate two sequences from a multiple alignment and show them side by side. The result can be useful to:
 
 1. find corresponding residue numbers between the aligned sequences;
-2. compress information about similarity in a graph.
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+2. compress information about similarity in a graph.
+
+Example of use:
+
+```
+python multiplalign_to_matrix.py -a testdata/DCP2_MAFFT.mfa -u "YEASX" -w "SCHPM" -o testdata/DCP2_MAFFT_matrix.txt
+python matrix_to_graph_alignment.py -m testdata/DCP2_MAFFT_matrix.txt -o testdata/Scer_vs_Spom_DCP2.pdf
+```
+From a multiple alignment (in jalview):
+
+<!-- ![jalview region of alignment](images/screenshot_jalview_dcp2.png) -->
+<img src="images/screenshot_jalview_dcp2.png" alt="jalview region of alignment" width="600">
+
+one can get the following image, with only two of the sequences highlighted, lower is S. cerevisiae, upper is S. pombe:
+
+![example of graphical output](testdata/Scer_vs_Spom_DCP2.png)
+
+More information in the pymultialign_description.md file.
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