The phrase "alignment by using the" is correct and usable in written English.
It can be used when discussing methods or processes that involve achieving alignment through a specific means or tool.
Example: "The team achieved alignment by using the new project management software to coordinate their efforts."
Alternatives: "alignment through the use of" or "alignment via the application of".
The codeml program of the PAML software package was used to detect positive selection in the CYP71C subfamily [ 39]. cDNA sequences were aligned based on protein alignment by using the RevTrans 1.4 server [ 40].
The 566 amino acid consensus sequence, named HA1-con, was generated from this alignment by using the most common amino acid at each position.
GRAAL, in contrast, computes a sequence-free pairwise alignment by using the notion of graphlet degree signatures.
Ortholog alignments were created using the transAlign program which increases the accuracy of a nucleotide alignment by using the corresponding amino acid alignment as a template [ 45].
The 16S rDNA sequences were obtained from the NCBI website [ 20] and trimmed after alignment by using the MEGA3 software package [ 32].
We conducted Bayesian, maximum-parsimony, and maximum-likelihood phylogenetic analyses on the combined alignment by using the avian HEV strain as an outgroup.
I generated an initial set of position-specific scoring matrices (PSSMs) from the resulting sequence alignments by using the BLOCKS server (http://bioinfo.weizmann.ac.il/blocks; [16]).
We performed multiple sequence alignments by using the ClustalX program (www.clustal.org/clustal2/).org/clustal2/
Phylogenetic trees and bootstrap analyses were performed with 100 alignments by using the SEQBOOT and CONSENSE programs of PHYLIP.
The values of Ka and Ks in BioMart were calculated for coding sequence alignments by using the maximum likelihood method implemented in PAML (Yang 1997).
For each dataset, novel sequences were manually added to previous alignments by using the ED program of the MUST package [ 24].
