From: A new ensemble coevolution system for detecting HIV-1 protein coevolution
Methods* | Statistical methodology | Updated | Ref |
---|---|---|---|
ASC/APC | Mutual information | 2007 | [34] |
BN | Bayesian network | 2007 | [35] |
CTMP | Continuous-time Markov model, phylogenetic tree | 2007 | [36] |
CoMap | Compensation coefficient, phylogenetic tree | 2007 | [37] |
Complementary | AA complementary matrix, Pearson coefficient | 2006 | [38] |
CMPro | 2D recursive neural networks | 2012 | [39] |
DCA | Maximum entropy model | 2011 | |
DNcon | Deep network, Bolzmann machines | 2012 | [40] |
GREMLIN | Maximum entropy model | 2013 | [41] |
Interdependency | Entropy, mutual information | 2004 | [42] |
LogR | Bayesian networks, APC | 2010 | [43] |
MI | Mutual information | 2012 | |
MIBP | Mutual information, physicochemical properties | 2011 | [46] |
Mutagenetic | Maximum likelihood mixed trees | 2005 | [10] |
NBZPX2 | Normal binary, ZRES | 2012 | [44] |
NCPS | Mutual information, sequence similarity | 2009 | [47] |
NNcon | Neural networks | 2009 | [48] |
PCC | Mutual information, Pearson’s coefficients | 2010 | [18] |
PSICOV | Sparse inverse covariance | 2012 | [49] |
PhysicoMI | Mutual information, physicochemical properties | 2012 | [6] |
PhyCMAP | Random forest, integer linear programming | 2013 | [50] |
RCW | Mutual information | 2007 | [51] |
Spidermonkey | MCMC Bayesian network, phylogenetic tree | 2008 | [52] |
SCA | Statistical free energy couplings | 2009 | [53] |
SVMcon | Support vector machine | 2006 | [54] |
ZRES | Mutual information | 2009 | [55] |