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An overview of the alignment strategy is presented in Figure S2.
A schematic diagram of the alignment strategy used in this study.
We confirmed that the phylogenies reconstructed from two versions of alignments were topologically equivalent, and ortholog-grouping was not biased arbitrarily because of the alignment strategy.
PSH has been recently been reported in Exhippolysmata [ 15], Lysmatella prima (Rhyne, unpublished) and Parhippolyte (Onaga & Fiedler, unpub)., a genus placed ancestrally to Lysmata, regardless of the alignment strategy.
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We have shown that the position of Exhippolysmata depends on the alignment strategy for 16S and the taxon sampling.
The placement of L. californica, which is considered a peppermint shrimp, is contingent to the alignment strategy of the 16S data.
Once all the conversions are performed, a key aspect for the efficient alignment of the reads is the alignment strategy.
This delaying procedure was incorporated in ClustalW in order to address the main drawback of the progressive alignment strategy: the greediness.
Despite the great potential of the embedded alignment strategies in answering a diverse set of biological questions, their computational costs are prohibitively expensive, a problem that arises out of the current method of generating and analyzing embedded sequences.
We report results from a study designed to assess the comparability of the two alignment strategies.
While the potential of chromatographic fingerprinting is undisputed, the choice of a suitable alignment strategy out of the algorithms available is not an easy task and represents a major obstruction for further acceptance and use of chromatographic profiling.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com