MSSYE_PQTREE_HEUR: Linearly encoded _PQ-tree_ of the _Drosophila_ ancestral...
In dorolin/rearrvisr: Detect, Classify, and Visualize Genome Rearrangements

Description Usage Format References See Also

A data set representing the Drosophila ancestral genome MSSYE with 8,973 markers on 20 Contiguous Ancestral Regions (CARs), reconstructed with the software ANGES (Jones et al. 2012). MSSYE represents the ancestor of the melanogaster subgroup (Drosophila 12 Genomes Consortium 2007; i.e., separating the group containing D. melanogaster, D. simulans, D. sechellia, D. yakuba, and D. erecta from the remainder of the Drosophila species). The genomes used to reconstruct the ancestral genome MSSYE were downloaded from Ensemble Release 91 (http://dec2017.archive.ensembl.org) and Ensemble Metazoa Release 37 (http://oct2017-metazoa.ensembl.org). Orthologs were identified with OMA standalone v2.2.0 (Altenhoff et al. 2015). See the package vignette for details.

1	MSSYE_PQTREE_HEUR

A data frame with a single column encoding an ancestral genome reconstruction as strings. The first row gives the name of the ancestor (preceded by >), followed by two rows for each ancestral genome segment (CAR). The first row of each set gives the CAR ID (preceded by #CAR), and the second row provides the PQ-tree structure of that CAR. The children of each node in the PQ-tree are enclosed by _P and P_ markups for P-nodes, or by _Q and Q_ markups for Q-nodes. Markers (i.e., ortholog IDs) that belong to a particular node are located between its corresponding markups. Markers with reversed orientation are preceded by a - sign. The opening (_P or _Q) and closing (P_ or Q_) markups can be nested to allow the representation of the hierarchical structure of the PQ-tree. For details on PQ-trees see Booth & Lueker 1976, Chauve & Tannier 2008, or the package vignette.

Altenhoff, A.M. et al. (2015). The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Research, 43, D240–D249. doi: 10.1093/nar/gku1158.

Booth, K.S. & Lueker, G.S. (1976). Testing for the consecutive ones property, interval graphs, and graph planarity using PQ-Tree algorithms. Journal of Computer and System Sciences, 13, 335–379. doi: 10.1016/S0022-0000(76)80045-1.

Chauve, C. & Tannier, E. (2008). A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLOS Computational Biology, 4, e1000234. doi: 10.1371/journal.pcbi.1000234.

Drosophila 12 Genomes Consortium (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450, 203–218. doi: 10.1038/nature06341.

Jones, B. R. et al. (2012). ANGES: reconstructing ANcestral GEnomeS maps. Bioinformatics, 28, 2388–2390. doi: 10.1093/bioinformatics/bts457

convertPQtree, computeRearrs, MEL_markers, SIM_markers, YAK_markers