v1.0.r031: JTT and big speedups on protein alignments25 Dec 2010, by Erick
I had a nice visit to the Eisen lab recently, and a number of good things happened. Two of those things were that Aaron Darling suggested that pplacer was too slow on proteins, and that it should be able to use the JTT model. After a bit of coding, pplacer is now about 5x faster on protein sequences, and JTT is working. These are now available in v1.0.r031.