This repository contains the work flow, scripts, and example files for the procedure of reconstructing ancestral genome from pairwise syntenic blocks using MLGO. Using this procedure, one could reconstruct the ancestral genomes for a set of selected species, even including species involving whole genome duplication or triplication. This procedure utilize the pairwise sytenic blocks and combine them into sytenic-block markers across all selected species. Then reconstruct the ancestral genome using Maximum Likelihood for Gene Order Analysis (MLGO).

The detailed description of work flow can be found in file "Work_flow.txt". Scripts used in this project can be found in the scripts/ directory. The example files can be found in the exampls/ directory.