Because Fastloc GPS location estimates vary, with a higher number of satellites generally yielding more accurate locations, we removed positions with <5 satellites [reported field-test spatial errors (mean ± S.D .: 8 satellites, 26 m ±19.2; 5 satellites, 64 m ±79.4] [13].
Nucleotide positions on the x-axis mark the removed positions upon transition to a reduced model.
We then progressively removed heteropecillous positions according to their increasing PIPn value; that is, we first removed positions that most likely violate the assumption of homogeneity over time of the CAT model.
The central 64 pots in the dense stand were used for measurements, and these pots were rotated every 10 d to remove position effects.
NJ tree was based on the distance calculation with JTT matrix [ 46] after removing position containing gaps (complete deletion option) for genes other than Zic genes, or after removing only in pairwise sequence comparisons (Pairwise deletion option) for Zic genes.
We found that in the resulting profile, even upon removing position specific heterogeneity for each individual mRNA, we still observed a sharp decrease in average ribosome density with codon position.
The lower AUC for SuRFR, however, is likely to represent the lowest estimate of SuRFR's performance, as by comparing regulatory variants with control variants matched by distance to TSS, we are effectively removing position from consideration.
Following [23], for each genotyped locus, we defined haplotypes according to sequence identity after removing positions for which only one sequence varied from the consensus.
The alignments of these proteins were concatenated into a single alignment, which was then trimmed to remove positions with gaps in more than 50% of the organisms.
Aligned sequences were filtered to remove positions with gaps as well as positions directly adjacent to gaps.
