PhyloQFold is en enhancement of McQFold.

If you use PhyloQFold for scientific work please read and cite

G. Doose, D. Metzler (2012) Bayesian Sampling of evolutionarily conserved RNA secondary
structures with pseudoknots *Bioinformatics* **28**: 2242-2248.

Please report all bugs in PhyloQFold to the developers of the program, Gero Doose and Dirk Metzler (e-mail addresses are given in the README accompanying the program).

The R file McQFold_param.R shows how Approximate
Bayesian Computation (ABC) can be applied to fit the paramters of the SCFG
used in McQFold and PhyloQFold to given RNA secondary structures with
pseudo-knots. It is assumed that secondary structures used as input for the
estimation procedure are independent
realizations of the stochastic model. This means that from each class of
homologous RNA sequences you should select one representative our a consensus
structure. (In our R file we show examples with simulated data.)
If you want to apply the ABC method given in our R file (also if you have real data),
you first need to compile the C++ program qsimul.cc
(e.g. with **g++ -o qsimul qsimul.cc -O2**),
which simulates RNA secondary structures with pseudo-knots according to the
grammar model, and you need to have the abc package installed in R.