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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