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To avoid any bias towards the more closely related set of five genomes from Saccharomyces ' sensu stricto' clade, the number of sequences to be included in the seed alignment from this group was reduced to a maximum of six.
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We used the alignments from this original dataset.
Next, the contig alignments from this assembly were evaluated to select clusters containing at least 5 reads.
The DIALIGN trees were preferred as they were supported by the alternative dendrograms, and because we rated the alignments from this algorithm most highly.
Could I figure out what his sexual alignment was from this conversation alone like the sexual spy Midori had trained us all to be?
Analyses were conducted on the full alignment, and from this also all combinations of pairwise comparisons between Xenopus species.
An alignment output from this source was used to create a dendrogram using TreeTop [ 45] with PHYLIP output (default parameters) at a node of the European Molecular Biology Network [ 47].
Additionally, Orb2 mutants present with disrupted mitotic spindle alignment; results from this study suggest that it may serve to promote the localization of aPKC [ 56].
For the analysis of characteristic sites in the DEXDc domain (SM00487), we downloaded the alignment for this domain from the SMART database (Letunic et al. 2009).
Poorly aligned regions from this alignment were removed with the Gblocks 0.91b program [ 74], using the default settings, except that allowable gap position was selected to half.
Alignments derived from this method have been shown to recapitulate many properties relevant to coevolution [15].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com