Tree of life in a gappy genomic era

0395574 - ÚBO 2014 CZ eng C - Conference Paper (international conference)
Martínková, Natália
Tree of life in a gappy genomic era.
Proceedings of the 8th Summer School in Computational Biology: From analysis of genomic data to clinical applications - case studies. Brno: Akademické nakladatelství CERM, 2012 - (Budinská, E.; Popovici, V.), s. 49-54. ISBN 978-80-7204-804-5.
[Summer School on Computational Biology /8./. Mikulov (CZ), 12.09.2012-15.09.2012]
Institutional support: RVO:68081766
Keywords : DNA sequence evolution * phylogeny * multilocus genotyping * supermatrix * supertree
Subject RIV: EG - Zoology

Increasing volume of publicly available DNA sequence data enables comprehensive studies that address integrative questions. For these projects, bioinformatic analysis requires advanced methods and computational infrestructure. I present the character of DNA sequence matrices for multilocus datasets, which contain large portions of missing data. A condition critical for analysis of multilocus data is that datasets for all loci or genes need to have partially overlapping taxon sets. The work-flow for analysing such data differs between supermatrix and supertree estimation of species trees. In the supermatrix approach, aligned sequences for all genes are concatenated and the species tree is estimated directly from a partitioned matrix. In the supertree approach, gene sequence alignments are used for inference of gene trees. Those are then combined into a species supertree. Smaller projects could benefit from utilising all available information in the supermatrix. Larger projects should rely on supertree methods for computational optimisation.
Permanent Link: http://hdl.handle.net/11104/0223585