AKtoolbox Files

=AKtoolbox 1.6=

AKtoolbox is a Matlab Toolbox for co-evolution analysis for protein 
Multiple Sequence Alignment (MSA).


===Introdction===
The aim of AK toolbox is to provide a set of Matlab functions, which are 
independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis of
MSA. At present, co-evolution methods available in this package are
Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset
Covariance(ELSC), Mutual Information (MI), Observed Minus Expected Square
method (OMES), McLanhlan Based Substitution Correlation (MCBASC) and
Direct Coupling Analysis (DCA). Enclosed in this package is also an 
archive of different Bioinformatics matrices. The folder CRY1 contains
some example files.


===Example usage===
    % Read in the example fasta file 'CRY1.fasta' at folder 'CRY1'.    
    % Notice that the structure returned by AKfastaread is different from
    % a structure returned by the fastaread.
    s=AKseqread('CRY1/CRY1.fasta')
    % Notice that since version 1.5, all sequence file parsing functions
    % are all merged into one function: 
    % AKseqread
    % Which supports FASTA, PHYLIP, CLUSTAL, PFAM, SELEX and FASTAQ format

    % Truncates MSA to a maximum identity betweeen sequences of 0.999, so 
    % that any pair of sequences will share no more than 99.9% of amino
    % acid sequences
    s=AKalnid(s,0.999)

    % Trim the MSA to the sequence with the phrase 'CRY1_ARATH' in its   
    % header so that all columns correspondent to a gap in this sequence
    % will be deleted
    s=AKtrimgap(s,'CRY1_ARATH')

    % SCA algorithm as used by Fodor & Aldrich (2004) with the background
    % frequency of gaps calculated by Residue Identity Percentage (RIP) as
    % proposed in Pascarella & Argos (1992)
    C_sca=AKsca(s,'fodor','rip');
    
    % The standard McBaSC algorithm, which ignore all gaps and is painfully
    % slow. You can instead use a non-standard algorithm, AKrca, which is
    % amazingly fast even without parallel processing.
    C_mcbasc=AKmcbasc(s);
    
    % A corrected version of Fodor's McBaSC algorithm
    C_rca=AKrca(seq,'fodor')
    
    % ELSC, MI, and OMES. Notice that there's no difference between 
    % inputting s and inputting s.seq here.
    C_elsc=AKelsc(s);
    C_MI=AKmi(s.seq);
    C_omes=AKomes(s.seq);
    
    % DCA method has been added since version 1.0. logR method has been 
    % added since version 1.6. These might take quite a while because the 
    % MSA is so long.
    C_dca=AKdca(s);
    C_logR=AKlogr(s);
   
    % AKsecstruct can extract sequence and secondary structure information
    % from PDB format or DSSP format coordinate files. It can also predict
    % secondary structure using very simple Chou-Fasman method.
    pdb=AKsecstruct('CRY1/1U3D.pdb')
    dssp=AKsecstruct('CRY1/1U3D.dssp')

See Contents.m for full list of provided functions as well as the
ChangeLog.


===license===
AKtoolbox is covered by two-clause BSD license:



Copyright (c) 2012-2014, Chengxin Zhang
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:

   * Redistributions of source code must retain the above copyright
     notice, this list of conditions and the following disclaimer.
   * Redistributions in binary form must reproduce the above copyright
     notice, this list of conditions and the following disclaimer in
     the documentation and/or other materials provided with the distribution

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.




"AKsubplot.m" is adopted from the "subtightplot.m" script also covered by
the two-clause BSD license:

Copyright (c) 2013-2014, Chengxin Zhang
Copyright (c) 2012, Felipe G. Nievinski
Copyright (c) 2010, Pekka Kumpulainen
Copyright (c) 2011, Nikolay S.



AKdca was rewrittened from "dca.m" script covered by this copyright notice.

Copyright 2011- by Andrea Pagnani and Martin Weigt
                   andrea.pagnani@gmail.com
                   martin.weigt@gmail.com
Permission is granted for anyone to copy, use, or modify this
software and accompanying documents for any uncommercial
purposes, provided this copyright notice is retained, and note is
made of any changes that have been made. This software and
documents are distributed without any warranty, express or
implied.