TY - JOUR AU - Auch, Alexander F. AU - Henz, Stefan R. AU - Holland, Barbara R. AU - Göker, Markus PY - 2006 DA - 2006/07/19 TI - Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences JO - BMC Bioinformatics SP - 350 VL - 7 IS - 1 AB - 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 δ value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study. SN - 1471-2105 UR - https://doi.org/10.1186/1471-2105-7-350 DO - 10.1186/1471-2105-7-350 ID - Auch2006 ER -