xfold

Introduction

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 algorithm.

As well as using phylogenetic StochasticContextFreeGrammars to predict RNA structure from multiple alignments (as with the Knudsen Hein algorithm), 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.

Getting xfold

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 package. See DownloadingDart for information on how to obtain.

Bug reports

See known issues with DART for bug reports and community wisdom.

-- IanHolmes - 23 Aug 2005