Datasets for use with POInT (the Polyploidy Orthology Inference Tool)

Supporting data for publications:

2019:

Conant, G. C. 2019. The continuing impact of an ancient polyploidy on the genomes of teleosts, bioRxiv.

• Gzipped TAR file consisting of nine files: 1) POInT's orthology inferences for the 5589 pillars analyzed (tab-delimited text), giving the estimated probability of all 28=256 possible orthology relationships at every pillar. 2-9) For each genome with the TGD, I give the synteny relationships seen in the estimated optimal ancestral order (tab-delimited text).
• POInT's orthology inferences for the 5589 pillars analyzed (tab-delimited text), giving the estimated probability of all 2^8=256 possible orthology relationships at every pillar..

A. Schoonmaker, Hao, Y., Bird, D. McK. and Conant, G. C. 2019 Confirmation of a single, shared triploidy in three species of parasitic nematodes, in preparation.

• POInT's orthology inferences for the 5316 triplicated pillars analyzed (tab-delimited text), giving the estimated probability of all 6^3=216 possible orthology relationships at every pillar..

2018:

Emery, M., M. M. S. Willis, Y. Hao, K. Barry, K. Oakgrove, Y. Peng, J. Schmutz, E. Lyons, J. C. Pires, P. P. Edger, and G. C. Conant. 2018. Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. PLoS Genetics 14: e1007267.

• README file describing these supplemental data
• Conditional probabilites for all loci for the At-alpha event
• Phylogenetic tree for the At-alpha event
• Conditional probabilites for all loci for the grass rho event
• Phylogenetic tree for the grass rho event
• Conditional probabilites for all loci for the yeast WGD
• Phylogenetic tree for the yeast WGD
• Link to original data posting at PLoS Genetics

2009:

Conant, G. C. and P. F. Stadler (2009) Solvent exposure imparts similar selective pressures across a range of yeast proteins, Molecular Biology and Evolution 26: 1155-1161. [Alignments, tree files, and rate files]