Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences

Background: Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs) between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Alexander F. Auch, Stefan R. Henz, Barbara R. Holland, Markus Göker
• Keywords: BMCBI 2006, Genome, Mitochondrial Genomes, Phylogenetic