Brief usage notes for MetaPSICOV
================================

To run MetaPSICOV you need to download and install PSIPRED, PSICOV, FreeContact, CCMpred and HHBLITS
separately. Please see relevant home pages for these packages for information on installation:
http://bioinf.cs.ucl.ac.uk/downloads/psipred
http://bioinf.cs.ucl.ac.uk/downloads/PSICOV
https://rostlab.org/owiki/index.php/FreeContact
https://bitbucket.org/soedinglab/ccmpred
ftp://toolkit.genzentrum.lmu.de/pub/HH-suite

To compile MetaPSICOV, untar, cd to src directory and run "make" followed by "make install".

A skeleton csh script called run_metapsicov is provided for running all of the MetaPSICOV steps.
Please consult the comments in this script (and the runpsipredandsolv script) for information on
how to customise the installation for your own setup.

Example usage:

run_metapsicov 5ptpA.fasta


If you use this software for your research, please cite the following reference:

MetaPSICOV: Combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
Jones, D.T., Singh, T., Kosciolek, T. & Tetchner, S. Bioinformatics (2014) doi:10.1093/bioinformatics/btu791
