Here, we take advantage of population genomics data to circumvent potential alignment issues to confirm the previous observations, and quantify rates of polymorphism and test for evidence of selection based on site frequency spectra (SFSs).
Our FST distance, which circumvents the multiple alignment step, correctly places the Sphaeroplea clade next to the Hydrodicton/Scenedesmus sister clade.
As a result, NY 252A was moved onto a new alignment that circumvented the runway to the south.
Motivation: Alignment-free methods for sequence comparison are increasingly used for genome analysis and phylogeny reconstruction; they circumvent various difficulties of traditional alignment-based approaches.
In the light of these findings, alignment-free distance-based reconstruction methods deserve special attention, as they circumvent potential pitfalls of the multiple alignment approach, especially with respect to divergent sequences, and can be advantageous in speed possibly without sacrificing reconstruction accuracy.
The problem of alignment can be circumvented by choosing a mesh periodicity which is smaller than the widths of the contact pad on the top of the LEDs (100 μm in our design).
We propose to circumvent this limitation using a subnetwork alignment approach.
We circumvent this problem by representing the alignment of a miRNA with an mRNA as a vector, where each element takes four possible values corresponding to a match, mismatch, gap, and GU wobble respectively.
Different gene prediction programs will often generate predicted gene structures that are dissimilar to each other and inconsistent with the homologous sequence alignments, introducing introns to circumvent frameshifts and premature stop codons.
Alignment-free methods were initially proposed to circumvent the issues of recombination and genetic shuffling that make alignment difficult [ 9], and they have attracted attention due to their computational efficiency [ 10] and accuracy [ 11].
