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Pipeline publication

[…] be aligned via Maximum Likelihood method (coat and tail genes), translated protein alignments were used to construct Neighbor-Joining trees in Unipro UGENE using the following parameters; a distance matrix model of F84, transition/transversion ratio of 2.0, and a bootstrap (replicate) value of 1000. These trees were confirmed using the Bayesian analysis of the MrBayes utility available in Unipro UGENE, in which a substitution model of HKY85 was used (Nst = 2) with default settings and a random seed number []. The per codon dN/dS ratios (ω) for the integrase, large terminase and portal genes were computed as a by-product of creating Bayesian phylogenetic trees from the respective genes using MrBayes [], where dN/dS was allowed to vary across codons. A gamma model was used for variation between sites, together with a proportion of invariant sites. Mean dN/dS values were reported for each triplet and then input to Excel to create the graph, including trend-line., The sequences for all M. catarrhalis prophages were used for a pan-genome comparison. To create a reference pan-genome of the prophages, the programme Panseq was run utilising default parameters []. Each prophage genome was aligned against this reference genome using the BLAST [] algorithm found with BLAST Ring Image Generator (BRIG) [] with the following parameters: all M. catarrhalis prophages represented a unique ring, except for the annotations for Mcat5 and Mcat6, from strains ATCC43617 and ATCC43617a, which were combined into a single output to avoid redundancy; an identity threshold between 90 and 100 % was selected for the image colour gradient generation; a default minimum threshold of 50 % was used for alignment; phages were ordered and colour coded according to their respective clades as described in the results section; and the output image was scaled to include a legend., MLST data for eight housekeeping genes, abcZ, adk, efp, fumC, glyβ, mutY, ppa, and trpE, were extracted […]

Pipeline specifications

Software tools MrBayes, Panseq, BRIG