Skip to main content

Table 4 Versions and sources of coevolution methods benchmarked

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

  Method Software package Version URL
Information-based MI infCalc v0.1.2 https://github.com/aavilahe/infcalc
  VI    
  MIj    
  MIHmin    
  MIw DCA “2011/12” http://dca.rice.edu/portal/dca/download
Direct DI    
  DI256 Code S1 in [68] “2013” http://doi.org/10.1371/journal.pcbi.1003176.s002
  DI32    
  DIplm plmDCA symmetric_v2 http://plmdca.csc.kth.se/
  PSICOV PSICOV V1.09 http://bioinfadmin.cs.ucl.ac.uk/downloads/PSICOV/
Phylogenetic CMPcor CoMap 1.5.1b5 http://home.gna.org/comap/doc/html/index.html
  CMPchg    
  CMPvol    
  CMPpol