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Corresponding topologies for each dataset were pruned from the Bayesian consensus tree using TreeEdit v1.0a10 [ 41] to maintain genealogical relationships found when all taxa's alleles were included.
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To measure their effect, the BLAST results of the 'Test case type3' dataset were pruned to hits of peptides from only 4000 randomly selected KO-families, referred to as the 'Selected_4K_KO_Hits'.
Replicate COI+cytB sequences were pruned from the dataset so that every haplotype in the phylogenetic analyses was unique.
The dataset was pruned by removal of highly similar paralogous or allelic protein sequences.
To test this possibility, the 3G dataset was pruned of all sequences not in the WG dataset.
For comparions between eukaryotic datasets and gammaproteobacteria data, this dataset was pruned to 50 taxa (Additional file 4).
However for large datasets, PSIKO seems to be superior, even if such a dataset is pruned based on, e.g., linkage disequilibrium.
For the individual nuclear and plastid analyses the dataset was pruned to include only taxa that are represented by the relevant gene region.
Loci under disequilibrium were pruned from the data matrix.
These outgroups were pruned from the resulting trees and not considered further.
The outgroup species were pruned from the trees in all the morphology and climatic preferences analyses.
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