James Pease and I just published a paper describing the problems that you might find when using BLAST for phylogenomics. The paper is here and published in Briefings in Bioinformatics.
We just published a new paper in BMC Evolutionary Biology looking at first steps in characterizing conflict, concordance, and gene duplications in phylogenomic datasets. See it here.
We have gotten the first data out from our Caryophyllales grant (together with 1KP data). We discuss gene and genome duplication, rates of molecular evolution and other fun things!
Yang, Y. M.J. Moore, S.F. Brockington, D.E. Soltis, G.K.-S. Wong, E.J. Carpenter, Y. Zhang, L. Chen, Z.-X. Yan, Y.-L. Xie, R.F. Sage, S. Covshoff, J.M. Hibberd, M.N. Nelson, and S.A. Smith. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Molecular Biology and Evolution.
With the support of the Caryophyllales grant, we have published (Sam Brockington and Ya Yang as co-first authors).
Brockington S.F., Y. Yang, F. Gandia-Herrero, S. Covshoff, J.M. Hibberd, R.F. Sage, G.K.-S. Wong, M.J. Moore and S.A. Smith. Lineage specific gene radiations underly the evolution of novel betalain pigmentation in Caryophyllales. New Phytologist.
We posted a bioarxiv version of our OpenTree paper that is in review here. Fun!
Ya Yang and Smith published a paper in MBE on orthology methods and phylogenomics. Check it here.
Cody and Stephen published a paper on the limitations of public data to construct large phylogenetic trees. Check it out here.