Reconstructing the architecture of the ancestral amniote genome

Warning

The data available on this webpage until December 12, 2012 contained a mistake, that has now been corrected.

Program

Available on demand to Cedric Chauve.

Ancestral blocks

Ancestral blocks (mapping on human genome and chicken genome).
Whole genome alignments used to compute genomic markers were downloaded from ftp.ensembl.org/pub/release-58/emf/ensembl-compara/pecan_16_amniota/.

Orthologous genes

Pairs of amniote-teleots orthologous genes.
Orthologous genes from the considered species were downloaded from ftp.ensembl.org/pub/release-58/emf/ensembl-compara/homologies.

Contiguous ancestral regions (CARs)

CARs (_Q indicates the beginning of a Q-node, Q_ the end of a Q-node, _P the beginning of a P-node and P_ the end of a P-node).
Weighted Ancestral Contiguous Sets (note: block i corresponds to markers 2i and 2i-1): Maximum Common Intervals, Block and Supported Adjacencies, Reliable Adjacencies, Combined and weighted.
List of all possible phylogenetic scores and the corresponding phylogenetic distribution.

Ancestral and double ancestral syntenies

Ancestral Syntenies/CSAM (Note: the coordinates 0-0 on the second genome indicatean infinite gap parameter).
Double Ancestral Syntenies (position on extant genomes: human, chicken).

Ancestral Synteny Graph

All possible edges (format: [edge_id]|[list of genomes containing the two blocks on a same chromosome] BLOCKS [block 1] [block 2]).
Non-discarded edges (format: [edge_id]|[list of genomes containing the two blocks on a same chromosome] BLOCKS [block 1] [block 2] CARS [CAR1] [CAR2]).
Connected components.