This page contains additional material for the paper "A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes".

Boreotheurian ancestor

For all datasets, we used a max_gap value of 100kb and we considered five possible values for the parameter min_len. For each value of min_len, we consider two datasets: the synteny blocks that are present in all 8 genomes (universal dataset, discussed in the paper) and the synteny blocks that are present at least in the 6 ingroups genomes (human, macaca, mouse, rat, dog, cow, almost universal dataset).

min_len=100kb

min_len=200kb

min_len=300kb

min_len=400kb

min_len=500kb

Ferungulate ancestor

  1. Coordinates of synteny blocks in human genome, from Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps (Supp. Material): FERUNG_COORDS.txt
  2. Extant genomes, from Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps (Supp. Material): FERUNG_PERM.txt

  3. For the files below, the format are similar than for the files above.
  4. All ancestral syntenies: FERUNG_ANCESTRAL_SYNTENIES.txt.
  5. Non-discarded ancestral syntenies used to compute the PQ-tree: FERUNG_PQ_SYNTENIES.txt.
  6. Generalized PQ-tree representing all ancestral syntenies: FERUNG_GPQ.txt.
  7. Chromosomal syntenies between the inferred CARs of the generalized PQ-tree and the 6 ingroup genomes: FERUNG_GPQ_CHR_SYNTENIES.txt.
  8. PQ-tree representing unambiguous ancestral genome architectures: FERUNG_PQ.txt.
  9. Chromosomal syntenies between the inferred CARs of the PQ-tree and the 4 ingroup genomes: FERUNG_PQ_CHR_SYNTENIES.txt.
  10. Support for ancestral adjacencies: FERUNG_SUPP_ADJ.txt.

  11. Using Ma et al. method Reconstructing contiguous regions of an ancestral genome.
    1. Config file: FERUNG_MA_CONFIG.txt.
    2. CARs Ancestor.car.
    3. Support for ancestral adjacencies: FERUNG_SUPP_MA_ADJ.txt.