We have selected genes differentially expressed between most distant clusters using J5 algorithm [ 21] with Jackknife option set to 4. We used the software implemented at the University of Pittsburg Cancer Institute with access through the Web interface [ 62].
To test for the occurrence of positive selection during the evolution of C4-specific NADP-me, three codon models were optimized using the software codeml, implemented in the PAML package (Yang 2007).
In order to investigate selective pressures that modeled the evolution of fru, we performed a relaxed branch-site test and a strict branch-site test [ 71, 72] using the software CODEML, implemented in PAML ver. 4 [ 73].
In the present work, the gene neighborhood was measured using the Syntonizer software (implemented in the MicroScope platform [ 29]), which is based on an exact graph-theoretical approach to measure synteny [ 30].
CDS were first detected using the Genemark software implemented in the CAAT-Box environment [ 55].
Data analysis were performed on the 5000 transcripts with the highest S.D. The number for neighbors for KNN imputation was equal to 10. GO analysis was performed using the appropriate software implemented in the Database for Annotation, Visualization and Integrated Discovery DAVIDD).
Read quality was checked with FastQC and reads were assembled de novo (including quality filtering and trimming) using the gsAssemler software implemented in Newbler version 2.6, with default parameters, except a seed step of 1 was used to improve sensitivity.
Linkage disequilibrium was calculated using the pwld software implemented in Stata.
Multiple protein sequence alignments were generated using the Muscle software implemented under MEGA5.
For the CoA, we used the appropriate software implemented in the Tigr MEV platform.
