DED: Database of Evolutionary Distances

DED: Database of Evolutionary Distances

A large database of homologous sequence alignments with good estimates of evolutionary distances can be a valuable resource for molecular evolutionary studies and phylogenetic research in particular. We recently created a database containing 159,921 transcripts from human, mouse, rat, zebrafish and fugu species. Approximately 1,000 homology groups were identified with the help of Ensembl homolo...

Evolutionary distances

Efficient Estimation of Evolutionary Distances

The advent of high throughput sequencers has lead to a dramatic increase in the size of available genomic data. Standard methods, which have worked well for many years, are not suitable for the analysis of big data sets, due to their reliance on a time-consuming alignment step. In this thesis, a new alignment-free approach for phylogeny reconstruction is introduced. The corresponding program, a...

Estimating Evolutionary Distances between Sequences

These notes accompany a lecture at the summer school on mathematics for bioinformatics, Centre de Recherches Mathematiques, Montreal, August 2003. I develop basic Markov models for sequence evolution and show how these may be used to estimate evolutionary divergences between sequences. I then discuss extensions of the basic model to situations where the evolutionary rate varies over time and fo...

Computing Distances between Evolutionary Trees

Supported in part by a CGAT (Canadian Genome Analysis and Technology) grant. Work done while the author was at McMaster University and University of Waterloo. Supported in part by NSF grant 9205982 and CGAT. Supported in part by NSERC Operating Grant OGP0046613 and CGAT. Supported in part by the NSERC Operating Grant OGP0046506 and CGAT. Supported in part by CGAT and NSERC Internation Fellowshi...