CHROnicle is a package dedicated to the reconstruction of the complete evolutionary history of genomes. It is based on the analysis of the marks accumulated over evolutionary time and left in the genomes by chromosomal rearrangements. CHROnicle is composed of four different programs: SynChro, PhyChro, ReChro and AnChro.

These four programs are independent but also intrinsically linked to each other because SynChro's output can be used as input for PhyChro, ReChro and AnChro; AnChro's output can be used as input for SynChro; and Anchro can use as input the output from SynChro, PhyChro (indirectly) and ReChro (ReChro is included in AnChro).

All four programs of CHROnicle can be run on any set of annotated genomes (from EMBL, GenBank or Fasta files). Before downloading any of them, you need to download the CHROnicle architecture, which contains toy examples as well as scripts that converts EMBL and GenBank files into the expected SynChro input format.

Then, download and unzip the 4 programs, or the one that you want to run, in your CHROnicle/Programs/ directory. Look at their individual page for details.


Reconstruction and visualization of Synteny blocks along Chromosomes.


Phylogenetic reconstruction based on Chromosomal rearrangement signal.

Not yet available - Waiting for the publication of the algorithm


Reconstruction of the Rearrangements along and between Chromosomes.


Reconstruction of the Ancestral Chromosome gene order.

All this work has been done during Guénola Drillon's Ph.D., whose the french thesis can be download here.

Last Update January 2016