1. Extant genomes: BOREO_PERM_400_a.txt

2. Ancestral syntenies.
   1. Format: Each line of a file represents an ancestral synteny: the first field is the weight of this synteny and the remaining fields are the labels of the synteny blocks that define it.
   2. All ancestral syntenies (non-conflicting adjacencies and maximum common intervals) detected during the first step of our method and used to compute the generalized PQ-tree: BOREO_ANCESTRAL_SYNTENIES_400_a.txt.
   3. Ancestral syntenies that were not discarded to remove ambiguities and are used to compute the PQ-tree: BOREO_PQ_SYNTENIES_400_a.txt.

3. Genome architectures: PQ-trees.
   1. Format: The P, Q and R nodes of a tree are indicated as follows: _P (resp. _Q, _R) indicates the beginning of a P (resp. Q, R) node and P_ (resp. Q_, R_) indicates the end of a P (resp. Q, R) node. The integers represent synteny block labels.
   2. Generalized PQ-tree representing all ancestral syntenies: BOREO_GPQ_400_a.txt.
   3. PQ-tree representing unambiguous ancestral genome architectures: BOREO_PQ_400_a.txt.

4. Conserved segements (segments of synteny blocks that are colinear in the ancestor and in the human genome).
   1. Format: Each line represents a conserved segment. The first field is the label of the conserved sement. The remaining fields are the synteny blocks that define this conserved segment.
   2. List of conserved segments BOREO_CS_400_a.txt.
   3. PQ-tree of these conserved segments BOREO_PQ_CS_400_a.txt

5. Chromosomal syntenies between the inferred CARs and the 6 ingroup genomes.
   1. Format: XX (YY) indicates that synteny block of label YY of the chromosome XX belong to a given CAR.
   2. Generalized PQ-tree BOREO_GPQ_CHR_SYNTENIES_400_a.txt.
   3. PQ-tree BOREO_PQ_CHR_SYNTENIES_400_a.txt.

6. Support of adjacencies.
   1. Format: Each line represents an adjacency that is present in all ancestral genome architectures defined by the PQ-tree. The first field is the weight of his adjacency (according to the weighting formula used in the paper). The two following fields are the two synteny blocks that define the adjacency. The fourth field is the number of ancestral syntenies that contain these two synteny blocks. The fifth field is the cumulated weight of these ancestral syntenies. The last field is the average weight of these syntenies.
   2. List of adjacencies and of their support BOREO_SUPP_ADJ_400_a.txt.

7. Results using Ma et al. method Reconstructing contiguous regions of an ancestral genome.
   1. Input files.
      • Coordinates of synteny blocks. The coordinates we use are not the real coordinates, but respect the chromosome locations and relative position and orientation of synteny blocks in our data. Moreover, the synteny blocks have been relabelled in order that they have consecutive numbers, which was required by the program. BOREO_SUPP_MA_COORDS_400_a.txt.
      • Config file. BOREO_SUPP_MA_CONFIG_400_a.txt.
   2. Results generated by the command
      createGenomeFile BOREO_SUPP_MA_CONFIG_400_a.txt BOREO_SUPP_MA_COORDS_400_a.txt > BOREO_SUPP_MA_PERM_400_a.txt
      Genome file: BOREO_SUPP_MA_PERM_400_a.txt Joins files: hg18.joins, rheMac2.joins, mm9.joins, rn4.joins, bosTau3.joins, canFam2.joins, monDom4.joins, galgal3.joins.
   3. Results generated by the command
      inferCars BOREO_SUPP_MA_CONFIG_400_a.txt BOREO_SUPP_MA_PERM_400_a.txt
      Joins in the ancestor Ancestor.joins and CARs Ancestor.car.
   4. Chromosomal syntenies between the inferred CARs and the 6 ingroup genomes: BOREO_MA_CHR_SYNTENIES_400_a.txt.
   5. Support of adjacencies: BOREO_SUPP_MA_ADJ_400_a.txt