CO-evolution Assessment by a Likelihood-free Approach
CoRe-Pa Nexus Format

CoRe-Pa [1] has a particular type of nexus file, which is composed by many blocks and sub-blocks of information to configure many parameters of the application. Coala is able to read this kind of file, but it just extract information only from the blocks listed in the example bellow:

#NEXUS
BEGIN TREES;
    TRANSLATE
        H0	H0,
	H1	H1,
	H2	A,
	H3	B,
	H4	C,
	P0	P0,
	P1	P2,
	P2	C1,
	P3	B1,
	P4	P1,
	P5	A2,
	P6	A1
	;
    TREE HOST = ((H2,H3)H1,H4)H0;
    TREE PARASITE = ((P2,P3)P1,(P5,P6)P4)P0;
ENDBLOCK;

BEGIN COPHYLOGENY;
    PHI
	C1	C,
	B1	B,
	A2	A,
	A1	A
	;
ENDBLOCK;
        
Block TREES

The block TREES has information about the pair of trees. The sub-block TRANSLATE contains pairs <labelnewick labelreal> which define the translation from the labels which appear in the newick represetantion to the real labels of the nodes of the trees. For instance, in the example above the real label of the host tree node H2 is A. The labels of each pair are separated by a TAB character (\t) and each pair is separated by a comma character (,).

After the sub-block TRANSLATE, the file contains two lines with the newick representation of host and parasite trees. Notice that, in this file format, the newick representation contains the labels of the internal nodes of the trees.

Block COPHYLOGENY

In the CoRe-Pa nexus file, the block COPHYLOGENY has many sub-blocks which configure the parameters of the application. In this block, Coala extracts information only from the sub-block PHI. This sub-block is composed by pairs of the type <leafparasite leafhost> where the elements are separated by a TAB character (\t) and each pair is separated by a comma character (,).

Notice that, the leaf labels that are listed in the pairs refer to the real labels and not to the labels that appear in the newick representation of the trees.

Important observations

The input file must contain only one pair of host and parasite trees.

The current version of Coala does not allow the association of one parasite leaf with many host leaves.


References
  1. D. Merkle, M. Middendorf, and N. Wieseke. A parameter-adaptive dynamic programming approach for inferring cophylogenies. BMC Bioinformatics, 11(Supplementary 1):10 pages, 2010.