follow this link

https://www.researchgate.net/post/Tool_for_identifying_synteny_blocks_among_multiple_pathogenomes

Try CIRCOS.. (http://circos.ca/)

The analysis of the synteny between two (or more species) is based in the evidence of collinearity of genomic features such as genes. In other words, two genomic regions are syntenic if contains elements in the same order (you can find a better definition at: http://genomevolution.org/wiki/index.php/Syntenic_regions).

Tools to analyze synteny are based in the search of homology between elements and further comparison of the position of these elements. There are several tools (DAGchainer, ColinearScan...) but my preferences are:

+ SyMap (http://www.agcol.arizona.edu/software/symap/). Very intuitive, easy to use (with GUI). It produces several outputs (figures, tables...).

+ MCScanX (http://chibba.pgml.uga.edu/mcscan2/). Perhaps not as intuitive as Symap, it contains very interesting tools such as the possibility to classify gene pairs in tandems or whole genome duplications. It also computes Ka, Ks substitution rates, so it can be very useful to estimate divergence rates.

Other interesting tool, if the genomes that you want to analyze have been published, is CoGe (http://genomevolution.org/CoGe/index.pl).

You can find a synteny map of macaque vs. human in Ensembl: http://www.ensembl.org/Macaca_mulatta/Location/Synteny?r=4:82972301-83097692

Check out various software and tools at http://bioinformaticsonline.com/blog/view/4574/tools-to-detect-synteny-blocks-regions-among-multiple-genomes