Generally, mismatches and gaps within alignments account for nucleotide substitutions and insertions and deletions (indels), respectively.
The bitscore is a measure of the quality of the alignment, also accounting for the length of the sequence overlap, and any gaps that have to be introduced to align the sequences.
Alignment positions, accounting for such functional specificity of the three enzymes in L. major were mapped and analyzed for their conservation.
She raised issues for design and analysis such as understanding the quality of the reference genome for alignment and accounting for the compositional nature of RNAseq samples (considering replication, treatment, organism tissues).
The program ClonalFrame (Didelot and Falush 2007, version 1.2) implements a Bayesian approach in which a single phylogeny is estimated for the entire genome alignment while accounting for homologous recombination.
Here, we generalize a hidden Markov model (HMM) to infer changes in phylogeny along multiple sequence alignments while accounting for rate heterogeneity; the hidden states refer to the unobserved phylogenic topology underlying the relatedness at a genomic location.
Such time-varying dipoles, or instantaneous dipoles, cannot orient themselves into alignment to account for the actual force of attraction, but they do induce properly aligned polarization in adjacent molecules, resulting in attractive forces.
When imperfect CNT/PP contact, CNT agglomerates and alignment are accounted for in the model the effective composite modulus predicted is in good agreement with the experimental data.
The SNPS that take S88 to be first to diverge in the original tree are in segments covered by putative recombination events 36 and 40 (Table S8), in which S88 appeared to gain DNA from a K-12 like donor, These two segments have 47% of the SNPs in recombinant segments in this 3 strain alignment, which accounts for their effect on the tree.
However, no commonly used alignment program accounts for within-sequence homology or SSM.
