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Second, the data we analyze is not a random sample of sequence space.
Third, our data set is a non-random sample of sequence space, with many biases whose extent is unknown.
Yet another study used phage display to examine the probability to find ATP binding proteins from a random sample of sequence space regardless the fold [47].
As these species do not have well-characterised genomes, it cannot be determined whether the amplified Retrosol fragments represent an unbiased random sample of sequence diversity.
We then searched for homologs of all sequences in the 50% identity clusters of the UniProt Reference Clusters database (UniRef50) [ 15], with the goal of obtaining a broad sample of sequence homologs.
Based on our large sample of sequence based markers and large pedigrees we have studied genome evolution in species from two tree genera, Salix and Populus by constructing linkage maps in Salix and aligning them to the Populus trichocarpa genome sequence.
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Our analyses used a convenience sample of sequences made publicly available by a variety of researchers from around the world, sampling at a variety of geographic scales.
Assuming neutral evolution, the coalescent process models the history of a population sample of sequences [59] by randomly generating a possible genealogy for the sequences.
Current methods of phylogenetic analysis provide stringent tests of monophyly given that an adequate sample of sequences are used in the analyses.
Every 200 generations, we took a random sample of sequences from the simulated population.
The low level of redundancy resulted in a sample of sequences derived from a wide range of biological functions.
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