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Table 1 List of methods benchmarked

From: Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species

  Method APC Re-weighting Reference Software package
Information-based MI No None [8, 71] infCalc
  VI    [65]  
  MIj    [8]  
  MIHmin     
  MIw   seq %id [9] DCA
Direct DI Yes seq %id, pseudocount   
  DI256    [68] Code S1 in [68]
  DI32     
  DIplm   seq %id [72] plmDCA
  PSICOV   Blosum, pseudocount [14] PSICOV
Phylogenetic CMPcor No Downsampling [10] CoMap
  CMPchg    [2]  
  CMPvol     
  CMPpol     
  1. Coevolution methods benchmarked fall into three categories. Information-based methods: MI: mutual information [71], VI: variation of information [65], MIj: MI divided by alignment column-pair entropy, MIHmin: MI divided by minimum column entropy [8], MIw: MI with adjusted amino acid probabilities. Direct methods: DI: direct information—MI with re-estimated joint probabilities [9], DI256, DI32: DI using Hopfield-Potts for dimensional reduction (256 and 32 patterns respectively) [68], DIplm: Frobenius norm of coupling matrices in 21-state Potts model using pseudolikelihood maximization [72], PSICOV: sparse inverse covariance estimation [14]. Phylogenetic methods: CoMap P-values for four analyses CMPcor: substitution correlation analysis [10], CMPpol for polarity compensation, CMPchg for charge compensation, CMPvol for volume compensation [2]