SEED was also used to determine orthologous proteins, using the standard parameters.
Maximum likelihood phylogenetic trees were created in MEGA using the standard parameters.
Using the standard parameters of the BESTFIT program, the two orthologues share 54% identity.
MOSAIK v1.0 was used to perform the alignments using the standard parameters.
We used OSLay then to compute an optimal syntenic layout of the contigs using the standard parameters of the implementation.
PGA was run using the standard parameters given in [ 11], for treecat the parameters were used as stated above.
CVs of the estimated TIACs were calculated for all cases and were precise (<25 %) or acceptable (<50%%), except for cases III and IV (Table 2) using the standard parameter set.
The PET image reconstruction was performed with the iterative Philips reconstruction software, using a 3D line-of-response time-of-flight blob-based algorithm using the standard parameter settings (3 iterations, 33 subsets, relaxation parameter: 1.0, transverse image matrix size: 144 × 144 voxels, voxel size: 4 × 4 × 4 mm3).
The population means and standard deviations for the individual time-integrated activity coefficients ã ref using the standard parameter values were 2.5 ± 4.3, 1.2 ± 0.3, 1.5 ± 0.5, 1.9 ± 1.1, 14.6 ± 4.1, and 0.9 ± 0.1 h for the tumor, kidneys, liver, spleen, whole body, and serum, respectively.
The software Haploview [37] was used to compute estimates of pair-wise LD by the standard D-prime method [38] and haplotype blocks defined by the confidence interval [39] using the standard parameter setting.
Simulations using the standard parameter set, but with the AER removed part-way during development, show the same result as when this manipulation is performed on developing limbs [40].
