Phylogenetic marker is a fragment (locus) of either coding or non-coding DNA which is used in phylogenetic reconstructions, i. e. which is known to have no or predictable variation within a given species, and which sequences are available for most or all species of a genus.
For example, the sequence of tef1 gene which is encoding the elongation factor -1alpha protein, contains three phylogenetic markers such as 4th and 5th introns (large and short, respectively) and 6th exon. Since these three markers have different power to resolve species, the BLAST result and its interpretation will strongly depend on which of these three markers is used. Unfortunately, there is not yet consistency in the Trichoderma community concerning to primers pairs (=fragments of the gene) which should be sequenced. Therefore it is often that sequences deposited in GenBank are significantly larger or shorter than any of tef1phylogenetic markers. As a consequence the similarity search by BLAST may provide an unclear result.
In order to increase the accuracy of the identification based on the similarity search (BLAST) we have created (i) a vouchered Multiloci Database of Phylogenetic Markers and (ii) TrichoMARK - a program which will first detect phylogenetic markers from the query sequence and then retrieve them for the following similarity search against the vouchered Multiloci Database of Phylogenetic Markers.