Automatic Barcode Gap Discovery (ABGD)

ABGD [22] version Jul 2014 was downloaded on Oct 14, 2015. While there is no universal barcoding gene available for phages, the 51 core genes shared by all of the 142 sequenced cyanophages were chosen as the dataset appropriate for this DNA barcoding analysis of a closely related virus community. Core genes of T4-like cyanophages display a signal of shared evolutionary history, as well as reduced effects of horizontal gene transfer evident in the flexible genome [64], and address part of the need for a dataset for which the evolution within a species follows that of a single unstructured population.

The program was run using the default Jukes-Cantor distance and 1.5X barcode gap options, with the -a command line option to output trees and text descriptions of all ABGD partitions. Prior divergence distances from 0.001 substitutions per site to 0.1 substitutions per site were tested, spanning common 5% divergence cutoffs used for analysis of microbial barcoding data [20, 21].