+
+Understanding Mussa
+===================
+
+
+Performance
+-----------
+
+Algorithm Behavior
+~~~~~~~~~~~~~~~~~~
+
+FIXME: Include seqcomp algorithm info.
+
+FIXME: Include transitivity info.
+
+Repeats
+~~~~~~~
+
+The algorithm Mussa uses to find conserved sequences is sensative to
+repeated DNA segments, which are naturally apart of many genomes. The
+problem with repeats, is that one repeat from one sequence can show up
+many times in another sequence. Every connection Mussa makes takes up
+memory, and it also takes time to store and process the results.
+
+The formula for the number of connections, C, that will be made for R
+instances of a single repeat (meaning R copies of one repeat in each
+sequence) and S sequences is:
+
+C = (R^2)[S(S-1)/2]
+
+Table of example situations:
+
+===== ===== =====
+ C R S
+===== ===== =====
+ 16 4 2
+ 48 4 3
+ 96 4 4
+ 160 4 5
+ 240 4 6
+ 336 4 7
+ 448 4 8
+ 24 2 4
+ 54 3 4
+ 96 4 4
+ 150 5 4
+ 216 6 4
+ 294 7 4
+ 384 8 4
+ 2500 50 2
+ 7500 50 3
+15000 50 4
+10000 100 2
+30000 100 3
+60000 100 4
+===== ===== =====
+
+After the connections, C, are found, they are passed on to the
+transitivity filter, which is a C^2 algorithm (FIXME: confirm
+algorithm is C^2). This means with 50 repeats in 2 sequences giving
+you a C of 2500, ends up with a C^2 of 6,250,000.
+
+**Conclusion: repeats cause the processing time of Mussa to skyrocket.**
+
+One, way to deal with a situation where you have lots of repeats in
+your sequences is to use shorter sequences lengths and/or repeat mask
+at least one of your sequences.
+
+Details
+-------
+
+Case: Conservation track suddenly stops
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+