The phrase "alignment along with the" is correct and usable in written English.
It can be used when discussing the coordination or agreement of elements in conjunction with something else.
Example: "The project requires alignment along with the established guidelines to ensure success."
Alternatives: "coordination with the" or "congruence alongside the".
This multiple sequence alignment along with the structure for each template are fed into model generation tools which construct models.
This transition kernel is based on the subtree-prune-and-regraft (SPR) operator but is modified to partially sample the alignment along with the tree.
This alignment, along with the entire LTP alignment for the domain Bacteria, was imported into the ape package (version 2.6-2) of the R environment for statistical computing (Paradis and Strimmer 2004); we then calculated an evolutionary distance matrix for each alignment using Kimura's two-parameter substitution model (Kimura 1980).
A color coding scheme illustrating the three dominant clades produced from the protein alignment along with those associated numerical clade designations is shown in Additional file 5.
The paired-alignments along with the PDB coordinates of the predicted structures are also available at Dryad: Ovchinnikov et al., 2014.
The two ClustalW alignments, along with the nucleotide sequences mapped to the protein alignments, were passed to the PAML module codeml (Yang 2007) to calculate the nucleotide substitution rates.
We aligned the contigs of each draft genome sequence against the ORFs from the complete genomes of either CFN42 or CIAT652, using both ungapped and gapped alignments, along with the reciprocal best hit criteria.
For example, Exon 1 is mapped to Chr1 A 1 -B 1 ; … ; Chr2 C 1 -D 1 ; …, where Chr1 A 1 -B 1 means Exon 1 is aligned from A 1 to B 1 in Chromosome 1 of UG. ② The stages " start" and " end" indicate the starting and ending of one combination of exon-alignments along with the chromosome direction.
Within a gene, the variant's position relative to the exon/intron structure is shown below the alignment, along with a text description of the variant.
Each generated alignment file can then be viewed individually or all alignment files (along with the original files) can be viewed simultaneously for comparison (Fig. 1B).
Thus, results from Group-I events indicate anisotropy in the region, along with the focal alignment.
