Multi-alignment of concatenated protein (or DNA) segments is a genome-scale, but not whole-genome approach. Its applicability depends on the scope of the phylogenetic study. When dealing with not-too-distantly related species it may yield more or less useful result. However, in a study covering many phyla it is very difficult, if not impossible, to collect a common set of conserved proteins. Moreover, the concatenation method can never lead to very convincing conclusion, as give or take a few proteins may change the result. The phylogenomics people have noticed this problem, see, e.g., O. Jeffroy, H. Brinkman, F. Delsuc, H. Philippe (2008) Phylogenomics: the beginning of incongruence? Trends in Genetics, 22(4): 225–231. An example from the Bacteria domain is the relationship of the closely related Shigella and Escherichia coli strains. Concatenation of different number of genes led to different way of mixing-up of the two groups, but CVTree gave unambiguous separation of the strains as different species in the same genus Escherichia, see: G.-H. Zuo, Z. Xu, B.L. Hao (2013) Shigella strains are not clones of Escherichia coli but sister species in the genus Escherichia. Genomics Proteomics Bioinformatics, 11: 61–65. In order to carry out multi-alignment of concatenated sequences, a postdoc or well-trained PhD student equipped with the corresponding software is required. In contrast, with genome sequencing becoming a common practice in many labs it costs no additional work for a bench-microbiologist to get phylogenetic and taxonomic information by using a convenient and publically available tool such as the CVTree web serve. Well, we would be glad to see comparison of CVTree phylogeny with multi-alignment of concatenated proteins if anyone finds a way to do it for so many diverse phyla, but we do not consider it as a doable job.
Authors present a new interactive tree-visualization tool which enables direct validation of taxonomic groups according to their monophyly.