The program finally evaluates, using the two indices implemented, each level of the dendrogram and saves the optimal partition of the tree for each index (see below).
They used the species accumulation index (implemented as our method 4) as one of their testing methods, but did not consider the practical constraints of existing reserves (e.g. over representing particular species and habitats).
We evaluated the heterogeneity indices implemented in CGITA with patient data from a cohort of ORC patients treated with definitive radiotherapy.
We used the proportion of nodes shared between each pair of trees (mtDNA + nucDNA, combined-data + mtDNA, and combined-data + nucDNA) as our index of similarity between trees, based on Rohlf's [ 86] consensus index (implemented in PAUP*).
A divergence value (based on the index implemented in Juekens et al. [ 40]) was calculated for each SNP, defined as the absolute value of the difference in the frequency of the major allele among ecotypes.
In order to putatively identify the sites of greatest differentiation between elevations, a divergence value based on the index implemented in Juekens et al. [ 40] was calculated for each SNP, defined as the absolute value of the difference in the frequency of the major allele among elevations.
As the observed number of alleles in a sample is highly dependent on the number of individuals sampled, we calculated the allelic richness corrected in the different sample sizes using a rarefaction index implemented in FSTAT [ 93]: thereby, the expected number of alleles in each sub-sample is calculated for the number of individuals present in the smallest sample.
The translation adaption (tAI) index implements a similar method, originally developed by dos Reis and colleagues [ 33, 34] (available from ).
Alternative indexes (Colless and Sackin indexes, as implemented in the package "apTreeshape," Bortolussi et al. 2006) provided identical results (tree imbalance intermediate between ERM and PDA models, not shown).
The stack flow uniformity and the standard flow deviation indexes are implemented to characterize the flow distributions in the stack and among the channels of FT-SOFC's, respectively.
