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All newly generated consensus sequences were screened again against the entire masked human genome and the next generation of consensus sequences was obtained from the new sets of identified repeats with incrementally expanded flanking regions.
Two independent runs with one cold and three heated chains each, were implemented for 1,000,000 generations with trees sampled every 100 generations; the consensus topology was generated after a burnin of 25%% of the retained trees.
The frozen scoring profiles (PSSMs) for the non-iterative profile-sequence alignments were generated in the same way as those used for generation of consensus sequences, except that a file containing the binary version of a PSSM was also stored [blastpgp option '-C PSSM binary)'].
They are also ideally used as anchor markers in molecular linkage maps and in generation of consensus maps across species and that can be highly saturated with DArT and SNP/genotyping by sequencing markers (GBS).
The clustering and generation of consensus sequences by heuristic methods were also completed within an hour.
Multiple sequence alignment, clustering, assembling and the generation of consensus were accomplished by StackPACK [ 29].
Variant calling and the generation of consensus sequences were carried out using the SAMtools program suite (http://samtools.sourceforge.net).net
This involved the generation of consensus sequences for OTUs consisting of more than one red algal family.
Combinatorial phage display selections are useful for the identification of high affinity binders and the generation of consensus motifs.
Sequence alignments used for phylogenetic analysis and for the generation of consensus sequences are available online as additional files.
The nominal group technique is a structured group information gathering process that aims to combine idea generation and consensus building into a single meeting [ 26].
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