After my rants and tirades against Editors and referees I decided that I would follow Ewan Birney and make my blog a bit more systematic. So this will be my lab notebook so I have proof of what I was thinking when.
So after reading a few textbooks my general opinion of some of the leading lights of phylogenetics is that they need to read a few more books. There is a whole lot of bad science out there and a complete failure to appreciate how evolution works.
Editor 1 is my favourite editor as he has cost me a PLoS One paper already and nearly another one in PeerJ. Anyway he suggested that FastTree is an inadequate method and I needed bootstraps. If he knew anything about FastTree he would know that for >100 sequences they suggest not using bootstraps but an estimator of the likelihoods instead which has a > 90% correlation to the bootstrap values. There is an alternative program which is PhyML and that says exactly the same. For trees of > 100 sequences compute the branch support using a Bayesian method.
You could create a bootstrap version by either running seqboot to create a bootstrap dataset for FastTree or by setting the bootstrap option in PhyML, but why would you? You would have to be stupid to do this when you get practically the same result from the internal estimator in minutes and the bootstrap calculations will take days. For example my H5 tree with > 4000 sequences cannot be run on PhyML. Removing the identical sequences reduces this to less that 3000 sequences BUT this will take 176 DAYS on the PhyML server. Running FastTree takes about half an hour.
The alignment file "H5_HA_4-10-15-2811_DNA_muscle.phylip" was uploaded, it contains 2811 taxons of 1926 characters.
The estimated computation time is : 176 day(s) 3 hour(s) 25 minute(s)
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It is therefore very clear that Editor 1 is stupid, unaware of current techniques and biased towards outdated methods inappropriate for the type of analysis I wish to carry out.