All pearl millet proteins were assessed for the presence of NBS domains (PF00931, NB-ARC) using the Hidden Markov Model based method implemented in hmmsearch (version 3.0 89 with an e-value cutoff = 1.
The maximum likelihood based method implemented in the codeml program of the PAML package (v3.15) [ 38] was used to detect positive selection as well as identifying positively selected sites, when the number of related sequences was sufficiently high.
Therefore, we used a more powerful maximum-likelihood based method, implemented in the CodeML subroutine of the software PAML [ 63] which allows the rates of ω = dN /dS to vary among codons [ 31, 64].
Ancestral distributions were estimated on the Bayesian consensus phylogram under Maximum Parsimony using MacClade v4.0 [ 66] and under a dispersal-vicariance event based method implemented in DIVA 1.1 [ 83].
In the present study, three methods were used: a distance-based method called ParaFit implemented in CopyCat [ 80] and topology (or tree -based metree -basedmethodsimplementednd TreeMap 3 (developed by Mine Charleston and available at http://sites.google.com/site/cophylogeny).
We first compared our method to the six well-regarded alignment-based methods implemented in the STAMP package, which represents state of the art research of motif comparision [8] and a more recently developed alignment-free method MoSta [18], for their ability to identify the TFBS motifs of structurally and/or evolutionarily related TFs using Dataset-1 by the "best-hit" method.
However, the sequence-based methods implemented in the phylogenomic studies have yielded phylogenetic trees that are similar to rRNA trees, which were demonstrated in the current study.
The effective population size of P. dulcis and P. orientalis and the magnitude of gene flow among species were inferred using coalescent-based methods implemented in Migrate-n (Beerli and Felsenstein 2001).
In terms of volume reproducibility, we found that manual delineation of malignant NSCLC lesions by a single imaging expert yielded VOIs with volumetric precision at least equivalent to semi-automatic segmentation methods including fixed threshold, adaptive threshold or cluster-based methods implemented in two previous publications in patients with lung and breast cancer [ 26, 27].
Among the many methods available, we chose the limited haplotype diversity method by Patil et al. [ 13] and extended by Zhang et al. [ 22], as implemented in the HapBlock software [ 23] (HapBlock), and the three LD-based methods implemented in the Haploview software [ 24]: the Gabriel et al. approach [ 15] (DprimeCI), the Solid Spine of LD (SSD), and the four gamete test [ 25] (4Gamete).
