Content of review 1, reviewed on December 13, 2014

Major Compulsory Revisions

My biggest concern is that the system may be access friendly only to the BGI. EXTRA effort needs to be taken to make the data access friendly to other researchers.

Specifically, it says that To submit the shells to SGE to run parallel jobs (NOTE: SGE represents the Linux cluster at BGI, not applicable in other places) "perl bin/qsub-sge.pl qsub-sge.pl --lines 1 --resource vf=3G -reqsub run.sh &"

It is not clear is this will work on any SGE or only on the one at BGI

Are there recommendations to make it work not only on SGE which is not available everywhere - for example I do not have it, neither the other labs I contacted to make sure this problem is objective.

Overall, better instructions are needed to run the scripts. Level of interest An exceptional article Quality of written English Acceptable Statistical review No, the manuscript does not need to be seen by a statistician. Declaration of competing interests I declare that I have no competing interests

Source

    © 2014 the Reviewer (CC-BY 4.0 - source).

References

    D., J. E., Siavash, M., J., A. A., Bo, L., Peter, H., Cai, L., W., H. S. Y., C., F. B., Benoit, N., T., H. J., Alexander, S., C., W. C., R., d. F. R., Alonzo, A., Nitish, N., Liang, L., Dave, B., Hans, E., V., E. S., Alexandros, S., P., M. D., Joel, C., L., B. E., Tandy, W., Wang, J., Pius, G. M. T., Guojie, Z. 2015. Phylogenomic analyses data of the avian phylogenomics project. GigaScience.