As an outsider to the viral phylogenetics community who just does some work for people in the community I get a pretty hard time from referees. If you are not part of the in crowd then they always find a reason why you have done something wrong. Some of my favourite examples are cladograms are wrong (then use the data I deposited to draw a phylogram if you want - which shows the same thing in more confusing detail). Some think you have to carry out a modeltest before building the tree (that would be the editor who wrote modeltest, and has managed to get it to 14,000 citations) whereas the next referee says modeltest is a worthless circular argument and pointless to carry out. The funniest was probably the figures are not clear to read, well they are vector graphic pdfs not bitmaps like all the ones you publish yourself so you could zoom them if you were not being obstructive and obfuscating.
The list of reasons goes on and on. The real question for an editor or referee to give a rejection is whether the science is right, not if it could be presented better. Wrong figures or writing are a source for corrections not for rejections. I have edited 120 papers and the default as an editor is to believe the scientist carried out with honesty and integrity and that if I was to do the same analysis I would get the same results. I believe in 100% transparency. That means; no anonymous referees, possibly post publication peer review (F1000 model), publishing all referees comments even for rejected papers.
All of this would be amusing rather than frustrating until I see that someone publishes the same idea a few months later and I lose any credit for it. For these reasons everything I ever do goes straight into to PeerJ repository so that I can always go that is a nice peer reviewed publication you have there but it is a shame I put mine in the repository before you even submitted yours, and isn't it strange that you were probably that anonymous reviewer that made sure my paper was rejected while you got your very similar one published. In my other interest as a lawyer they have a name for this practice. They call it fraud.