Reconstructing Contiguous Regions of an Ancestral Genome

This site contains the source code and resultant data from our paper:

Ma, J., Zhang, L., Suh, B.B., Raney, B.J., Burhans, R.C., Kent, W.J., Blanchette, M., Haussler, D., and Miller, W. 2006. Reconstructing Contiguous Regions of an Ancestral Genome. Genome Research. Published online before print Sept 18, 2006.

We are maintaining two versions of our source code and data. The frozen version, which is static, is a snapshot of our code and data as of paper publication. The latest version, which will change over time, contains our most recent bug fixes and enhancements.

Output Data

The output data includes the Orthology Blocks, Conserved Segments, Contiguous Ancestral Regions, a file that describes which species support each ancestral join, and our list of micro-inversions.

bzipped tar file of output data latest release 2006-Jun-16

bzipped tar file of output data frozen release 2006-Jun-16

Software

bzipped tar file of source code latest release 2006-Jun-16

bzipped tar file of source code frozen release 2006-Jun-16

Input Data

bzipped tar file of nets and chains (1.5GB; 7.7GB uncompressed) frozen release 2006-Jun-16

Simulated Datasets

bzipped tar file of simulated datasets frozen release 2006-Jun-16