Jane [1] and TreeMap [2] use the same type of nexus file (also known as tanglegram .tgl). This kind of file has the following structure:

#NEXUS
BEGIN HOST;
    TREE HOST = ((A,B),C);
ENDBLOCK;
BEGIN PARASITE;
    TREE PARASITE = ((A1,A2),(B1,C1));
ENDBLOCK;
BEGIN DISTRIBUTION;
    RANGE
        C1 : C, B1 : B, A2 : A, A1 : A;
ENDBLOCK;
        

As we can see in the example above, the this nexus file format is composed of three blocks of information.

This block defines the host tree. This tree must be given in newick format. Usually, in this kind of file the newick format does not contains the labels of the internal nodes.

This block defines the parasite tree. This tree must be given in newick format. Usually, in this kind of file the newick format does not contains the labels of the internal nodes.

This block defines the association among host and parasite leaves. This list of assocations is composed by pairs <Parasite Label : Host Label> separated by commas (,). In this file format, the separator is a collon character (:).

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.

For technical reasons, Coala create label names for the internal nodes of the trees. These labels have the format #HX and #PX, respectively, for host and parasite trees, where X is an integer number. Thus, the user should avoid the use of labels like #H1, #H2, #P1, #P2, etc.

1. C. Conow, D. Fielder, Y. Ovadia, and R. Libeskind-Hadas. Jane: a new tool for the cophylogeny reconstruction problem. Algorithms for Molecular Biology, 5(16):10 pages, 2010.
   
   
2. R. D. M. Page. Parallel phylogenies: reconstructing the history of host-parasite assemblages. Cladistics, 10(2):155–173, 1994.

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