Software
http://wwwfgu.anat.ox.ac.uk/~gerton/
HMMoC
- generates efficient C++ code from a high-level description of a hidden Markov model
GRAPe/a> - Efficient and accurate whole-genome re-alignment tool; annotates alignments with reliability scores
IPS/a> - Python script to identify indel-conserved regions ("indel-purified segments")