Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling.

ABSTRACT: The constant accumulation of sequence data poses new computational and methodological challenges for phylogenetic inference, since multiple sequence alignments grow both in the horizontal (number of base pairs, phylogenomic alignments) as well as vertical (number of taxa) dimension. Put aside the ongoing controversial discussion about appropriate models, partitioning schemes, and assembly methods for phylogenomic alignments, coupled with the high computational cost to infer these, for many organismic groups, a sufficient number of taxa is often exclusively available from one or just a few genes (e.g., rbcL, matK, rDNA). In this paper we address scalability of Maximum-Likelihood-based phylogeny reconstruction with respect to the number of taxa by example of several large nested single-gene

SUBMITTER: Stamatakis A 

PROVIDER: S-EPMC2880847 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature