We limited the search for tandem duplications to sequences with ≤75% of the average evolutionary distance from terminal nodes to an approximate midpoint root in the phylogeny, the maximum search depth.
The maximum search time is T max.
We calculated proximity to traffic by measuring the distance from geocoded home address to the nearest major roadway (interstate, state, or county highway or major arterial), with a maximum search radius of 150 m.
Peak detection using maxima search.
Phylogenetic relationships between the diplogastrid taxa were assessed based on 471 bp of the SSU sequences with the help of the PAUP*4.0b10 software using maximum parsimony (MP, heuristic search, gaps as 5th state), neighbour-joining (NJ, BioNJ algorithm with maximum likelihood distances) methods, and heuristic search using maximum likelihood (ML) as optimality criterion [ 28, 42].
Although the minimum distance allowed between interacting SNPs in the analysis was 100 kb, it is interesting that the maximum distance between two interacting SNPs was less than 2 Mb given that the maximum possible distance in the search space is 10 Mb.
Genetic distances between species are reported as minimum pairwise distances, while intraspecific variation is reported as maximum pairwise distances.
Linear discriminant analysis searches for a vector, w T, called a discriminant transformation function that results in the minimum intraclass and the maximum interclass distances when a data is projected onto it [ 28].
At each iteration, k, the swarm radius, δ k), is considered to be the maximum Euclidean distance, in n-dimensional search space, of any particle from the global best solution as follows: delta (k)={displaystyle underset{iin left{1,2,dots, Nright}}{ max }}leftVert {x}_i k -{G}_{best}rightVert (14).
We used mostly default BWA options for single-end mapping, with iterative search disabled and allowing a maximum edit distance of two.
