Multiple Sequence Optimization Alignment by Heuristic Methods is the third of 10 lectures on Biological Sequence Analysis [BSA], I give at ANU, Canberra, Australia in September to December 2018. BSA is a huge field since sequences are presently so abundant. Multiple Sequence Analysis only took off in the late 80s after Pairwise Sequence Analysis had been enough until then.
Jotun will discuss heuristic methods used to align a large number of sequences. These are the programs that the users know. There is no guarantee for their performance. They are empirically tested against bench marks that is has been manually made to fit what a biologist would like often using extra data such as protein structure. Some of these programs (like Clustal, MAFFT, PRANK,.) have developed over decades and articles describing them often have focus on how to run the program. Jotun will in this lecture try to list key tricks used in these programs allowing them to analyze such large data sets, classify the objectives of multiple alignment, go through some key programs and finally suggest some problems that might be worth to work on.
Preliminary slides can be found here.