A set of protein pairs was used for testing alignments and selected so that there should be some structural similarity, but little sequence similarity.
As reference score (RS) we used the sum-of-pair scores, which denote the proportion of amino acid pairs that are aligned in the test alignment the same way as in the reference.
The sum-of-pairs score (SPS) is the proportion of aligned pairs of nucleotides/amino-acids from the true alignment that are also aligned together in the test alignment.
In [ 22] we used the BALISCORE, which computes the fraction of identities between a trusted reference alignment and a test alignment, where identity is defined as the averaged sequence identity over all aligned pairs of sequences.
We tested alignment sensitivity by repeating phylogenetic analyses on a data set in which ambiguously aligned regions were removed by excluding positions in each direction until we came to nucleotides that were invariant in all taxa in the analysis [ 68].
In silico PT data sets can be generated from simulated or actual sequencing data and are used to test alignment through variant detection and annotation steps.
In this case report, we apply these frameworks to test alignment with practitioner experience and to examine the degree to which they contribute to the understanding of the case.
Suppose we have a test alignment of N sequences and M blocks.
First, clustering optimization enabled us to test alignment programs and distance functions and to identify the best approach es).
