Editing Probabilistic context-free grammar (section)

===== Pfold improvements on the KH-99 algorithm =====
PCFG based approaches are desired to be scalable and general enough. Compromising speed for accuracy needs to as minimal as possible. Pfold addresses the limitations of the KH-99 algorithm with respect to scalability, gaps, speed and accuracy.<ref name="Knudsen 2003" /> 
*In Pfold gaps are treated as unknown. In this sense the probability of a gapped column equals that of an ungapped one. 
*In Pfold the tree {{mvar|T}} is calculated prior to structure prediction through neighbor joining and not by maximum likelihood through the PCFG grammar. Only the branch lengths are adjusted to maximum likelihood estimates. 
*An assumption of Pfold is that all sequences have the same structure. Sequence identity threshold and allowing a 1% probability that any nucleotide becomes another limit the performance deterioration due to alignment errors.