Additional file 4.

Figure S2. Phylogenetic tree of Arabidopsis thaliana and Capsella rubella SLEEPERS. We estimated the non-synonymous substitution rate (Ka), synonymous substitution rate (Ks) and Ka/Ks values between DAYSLEEPER and CYTOSLEEPER and their respective homologs in Capsella rubella. We used the coding sequences of the genes that we found using BLASTN with the DAYLEEPER and CYTOSLEEPER coding sequences in the Phytozome [19]Capsella rubella genomic database. We found hits for both queries with scores of 2786 and 1891 respectively both with an E-value of 0. A FASTA file containing the unaligned coding sequences were used in the online “Ka/Ks Calculation tool” of the Bergen Center for Computational Science (http://services.cbu.uib.no/tools/kaks) [41,42]. The values in the phylogenetic tree represent the calculated Ka/Ks ratio’s.

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Knip et al. BMC Plant Biology 2012 12:192   doi:10.1186/1471-2229-12-192