BACKGROUND: Identifying syntenic regions, i.e., blocks of genes or other markers 
with evolutionary conserved order, and quantifying evolutionary relatedness 
between genomes in terms of chromosomal rearrangements is one of the central 
goals in comparative genomics. However, the analysis of synteny and the 
resulting assessment of genome rearrangements are sensitive to the choice of a 
number of arbitrary parameters that affect the detection of synteny blocks. In 
particular, the choice of a set of markers and the effect of different 
aggregation strategies, which enable coarse graining of synteny blocks and 
exclusion of micro-rearrangements, need to be assessed. Therefore, existing 
tools and resources that facilitate identification, visualization and analysis 
of synteny need to be further improved to provide a flexible platform for such 
analysis, especially in the context of multiple genomes.
RESULTS: We present a new tool, Cinteny, for fast identification and analysis of 
synteny with different sets of markers and various levels of coarse graining of 
syntenic blocks. Using Hannenhalli-Pevzner approach and its extensions, Cinteny 
also enables interactive determination of evolutionary relationships between 
genomes in terms of the number of rearrangements (the reversal distance). In 
particular, Cinteny provides: i) integration of synteny browsing with assessment 
of evolutionary distances for multiple genomes; ii) flexibility to adjust the 
parameters and re-compute the results on-the-fly; iii) ability to work with user 
provided data, such as orthologous genes, sequence tags or other conserved 
markers. In addition, Cinteny provides many annotated mammalian, invertebrate 
and fungal genomes that are pre-loaded and available for analysis at 
http://cinteny.cchmc.org.
CONCLUSION: Cinteny allows one to automatically compare multiple genomes and 
perform sensitivity analysis for synteny block detection and for the subsequent 
computation of reversal distances. Cinteny can also be used to interactively 
browse syntenic blocks conserved in multiple genomes, to facilitate genome 
annotation and validation of assemblies for newly sequenced genomes, and to 
construct and assess phylogenomic trees.