The phylogenetic trees were inferred using the Bayesian algorithm built in the software MrBayes, version 3.2.2 (Ronquist et al. 2012).
In this study, the NOA is built using the algorithm described in[27].
For inferring intraspecific evolution, networks of haplotypes sampled from populations of R. solani AG-3 were built using the algorithm recommended by Posada & Crandall [ 26].
The pregnancy period was built using the algorithm developed by Li et al., which was shown to correctly classify medication exposure status in most live born deliveries with a sensitivity and positive predictive value of ≥95% and a specificity and negative predictive value of almost 100% [ 17].
Relevance networks were built by using the algorithm indicated by the manufacturer.
High-quality reads were aligned to the human genome, Build 36.2, RefSeq transcript database, Release 22 [81], Unigene Hs, build 215 [82] using the algorithm GMAP [55] and the software system Alpheus® [48], with adjustments for short SBS reads (oligomer overlap interval = 3 nt, identities ≥34/36 or 94%).
In brief, TF-binding regions were identified by using the peak-finding algorithm built into the NimbleScan software (Roche NimbleGen).
Two simple aggregation-accretion algorithms were used to generate aggregates used in our simulations; the algorithms build the ballistic particle-cluster aggregate (BPCA) and the ballistic cluster-cluster aggregate (BCCA) (Meakin, 1983).
The neural network consisted of one hidden layer and the number of processing elements (neurons) was chosen using the built in genetic algorithm routine.
pic2recipe was built using the Food-101 Data Set, a food-identifying algorithm built by Swiss scientists in 2014, using a database of 101,000 food images.
