AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for 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), Direct-coupling analysis (DCA) and logR. Enclosed in this package is also an archive of different Bioinformatics matrices.

AKtoolbox_1.6\AKalnid.m
.............\AKalnread.m
.............\AKdca.m
.............\AKdealign.m
.............\AKeig.m
.............\AKelsc.m
.............\AKlinereg.m
.............\AKlogr.m
.............\AKmcbasc.m
.............\AKmi.m
.............\AKmsarnd.m
.............\AKnwalign.m
.............\AKomes.m
.............\AKrca.m
.............\AKsca.m
.............\AKsecstruct.m
.............\AKseqread.m
.............\AKseqwrite.m
.............\AKsquareform.m
.............\AKsubplot.m
.............\AKtrimgap.m
.............\CRY1
.............\....\1U3D.dssp
.............\....\1U3D.pdb
.............\....\CRY1.fasta
.............\Contents.m
.............\license.txt
.............\logr.c
.............\logr.dll
.............\logr.m
.............\logr.mexa64
.............\logr.mexglx
.............\logr.mexmaci
.............\logr.mexmaci64
.............\logr.mexw32
.............\logr.mexw64
.............\private
.............\.......\McLanchlan.m
.............\.......\blosum100.m
.............\.......\blosum30.m
.............\.......\blosum35.m
.............\.......\blosum40.m
.............\.......\blosum45.m
.............\.......\blosum50.m
.............\.......\blosum55.m
.............\.......\blosum60.m
.............\.......\blosum62.m
.............\.......\blosum65.m
.............\.......\blosum70.m
.............\.......\blosum75.m
.............\.......\blosum80.m
.............\.......\blosum85.m
.............\.......\blosum90.m
.............\.......\blosumn.m
.............\.......\dayhoff.m
.............\.......\gonnet.m
.............\.......\identity.m
.............\.......\match.m
.............\.......\meansm.m
.............\.......\nuc42.m
.............\.......\nuc44.m
.............\.......\pam10.m
.............\.......\pam100.m
.............\.......\pam110.m
.............\.......\pam120.m
.............\.......\pam120cdi.m
.............\.......\pam130.m
.............\.......\pam140.m
.............\.......\pam150.m
.............\.......\pam160.m
.............\.......\pam160cdi.m
.............\.......\pam170.m
.............\.......\pam180.m
.............\.......\pam190.m
.............\.......\pam20.m
.............\.......\pam200.m
.............\.......\pam200cdi.m
.............\.......\pam210.m
.............\.......\pam220.m
.............\.......\pam230.m
.............\.......\pam240.m
.............\.......\pam250.m
.............\.......\pam250cdi.m
.............\.......\pam260.m
.............\.......\pam270.m
.............\.......\pam280.m
.............\.......\pam290.m
.............\.......\pam30.m
.............\.......\pam300.m
.............\.......\pam310.m
.............\.......\pam320.m
.............\.......\pam330.m
.............\.......\pam340.m
.............\.......\pam350.m
.............\.......\pam360.m
.............\.......\pam370.m
.............\.......\pam380.m
.............\.......\pam390.m
.............\.......\pam40.m
.............\.......\pam400.m

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