Syn_MRL

Syn-MRL is a way to reconstruct phylogenies based on microsynteny information. It combines synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference. Syn-MRL approach proceeds by encoding phylogenomic synteny pattern profiles, obtained from a clustering of the synteny network , into a binary data matrix. We analyze this data matrix using a standard maximum likelihood (ML) reconstruction program under a binary model (here we use Mk).

Such a process is similar to the MRL (Matrix Representation with Likelihood) supertree method (which uses the same data matrix as Matrix Representation with Parsimony, but with ML-based inference, yielding higher accuracy), except that MRL is based on a set of input trees, in contrast with our synteny matrix, which is based on synteny clusters. 

 

 To perform such an analysis, we need to binarize all synteny network profiles, and prepare a phylip format matrix for tree inference. 

After Phylogenomic-Profiling, we have an output file looks like this:

(for convenience, we call this file clusters_profiled.txt): 

 Dana Dere Dgri Dism Dmel Domj Dpse Drpe Dsec Dvir Dwil Dyak
1 3 3 3 3 3 3 3 3 3 4 3 3
2 0 3 3 3 3 3 3 3 3 3 2 3
3 2 2 2 2 2 2 2 2 2 2 2 2
4 0 3 3 3 3 3 3 3 3 3 3 3
5 2 2 2 2 2 2 2 2 2 2 2 2

We use this ouput file as the input to generate the binary data matrix. 

Usage: 'Rscript  BinaryDataandTranspose.r  clusters_profiled.txt 1'  

Don't forget the number 1, which means to use all the clusters.

Afterwards, you will obtain a file surfixed with '_binary_transposed'. Add #taxa and #columns(which is the number of clusters) in the first row. (See a sample here).

This matrix can be used for tree inference, here using IQTREE as example: 

iqtree -s binary_transposed_matrix \
-bb 1000 -alrt 1000 -nt 10 -m MK+R+FO -redo -st MORPH