xfold

Introduction

The xfold program is a derivative of the xgram software for sequence analysis with phylo grammars. The only special feature of xfold over xgram is that xfold has several useful preset grammars for RNA analysis hardcoded into the executable. These grammars can be loaded and saved just like any other xgram format phylo-grammar.

XFold's default preset an implementation of the KnudsenHein algorithm. As well as using phylogenetic StochasticContextFreeGrammars to predict RNA structure from multiple alignments, it can use the HolmesRubin Expectation-Maximisation algorithm to quickly estimate all parameters (including evolutionary rates) from training data.

Getting xfold

XFold 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