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Therefore, seven sequences (from the C4 NADP-me genera Aristida, Arundinella, Mesosetum, Stipagrostis, Streptostachys, and Tatianyx) were removed from the data set and manually pruned from the topology.
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We ran SCONE on each of the multiple-sequence alignments, using a species tree obtained from the UCSC Genome Bioinformatics site [ 80] that we manually pruned so that it contained only placental mammals.
The top 1000 sequences from both searches were aligned using Clustal Omega (Sievers et al., 2011) and manually pruned in Jalview (Waterhouse et al., 2009) to eliminate sequences with large insertions or deletions.
To assign genes to mapped ChIP peaks, we used intersectBed and closestBed and subsequently manually pruned the gene lists.
Phylogeny was pruned from Moreau et al. (2006).
Loci under disequilibrium were pruned from the data matrix.
Hence, it must be pruned from the array PP.
The outermost outgroup was pruned from the tree.
Finally, intervals are pruned from the search space, if possible.
It was pruned from the resulting trees and discarded from all subsequent analyses.
The subnet based on extended k-core is pruned from the complex.
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