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 Author:  Ruriko Yoshida
 Date:    June 21st, 2006
 Update:  August 15th, 2013
 Program: This is software for the coevolution data analysis.

 Input:  Host tree and Parasite tree in newick format.

 Output:  Sampling data points in R^2 and the p-value of codivergence.
 
 Installation: Just type:
   make
   make all

 Uninstall: Just type:
   make clean

  Softwear: There are two software, namely samplingData and samplingDataNew.
     samplingData:   It computes the set of MRCA pairs and also computes
                     the p-values using ALL pairwise distances.
     samplingDataNew:It computes the set of MRCA pairs and also computes
                     the p-values using the MRCA pairs.

 Default invocation:

 ./samplingData H-tree P-tree mapFile randomTreeH randomTreeP -o outfile

 where H-tree is the host tree, P-tree is the parasite tree, mapFile 
 indicates a relation between each host and each parasite, and outfile.res
 is the output file for the set of MRCA pairs.  randomTreeH and randomTreeP are lists of random trees.

Example:
./samplingDataNew plant-endo/plantfullmax26.phy plant-endo/endofullmax26.phy plant-endo/full26.rel plant-endo/plantfullmax26.rand0005 plant-endo/endofullmax26.rand0005 -o out

Data:
There are two types of data in directories, plant-endo and gopher-lice.

plant-endo: There are data sets used for our paper, C. Schardl, et al, 2007.  

    TH                 TP                  rel        TH random trees       TP random trees.
plantXmax26.phy  endoXmax26.phy  X26.rel  plantXmax26.randp  endoXmax26.randp (p = 1, 05 001 0005 for SF = 1, 0.5, 0.001, and 0.0005.  Also X = full, t1, t2, t3, or t4 for the type of data sets.)

If a file name has "ave" then they are sampled trees from the likelihood function via MCMC.

gopher-lice:  They are data from Hafner and Page.



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