The xfold program
is a derivative of the xrate software
for sequence analysis with phylo grammars
Essentially, xfold is just the combination of the generic xrate program and the xrate format
grammar corresponding to the KnudsenHein
As well as using phylogenetic StochasticContextFreeGrammars
to predict RNA structure from multiple alignments (as with the KnudsenHein
xfold/xrate can perform several related functions, such as using the HolmesRubin
Expectation-Maximisation algorithm to quickly estimate all parameters
(including evolutionary rates) from training data, or reconstructing ancestral RNA sequences.
Currently, xfold is not distributed as a separate executable; rather, one can use the xrate program with the "--preset pfold" option, or alternatively, load a grammar from an external file (such as this one: DartGrammar:pfold.eg
XRate (along with the above-linked grammar file) is available as part of the DART
for information on how to obtain.
See known issues with DART
for bug reports and community wisdom.
- 23 Aug 2005