2.7 | Phylogenetic tree reconstruction
Protein sequences of all single-copy gene families were aligned using MUSCLE (Edgar, 2004), and the alignments of each gene family were concatenated into a super-alignment matrix. These data matrices were used for maximum likelihood phylogenetic analyses by RAxML (http://sco.h-its.org/exelixis/web/software/raxml/index.html) with a bootstrap value of 100. A. thaliana was designated as outgroups. The Venn diagram was constructed to display the number of gene families that were shared among four Poaceae species (A. tauschii , T. aestivum , H. vulgare , and S. cereale ) clustered into one group of the phylogenetic tree.