The phrase "aligned based on the" is correct and usable in written English.
It can be used when discussing how things are organized or coordinated according to specific criteria or standards.
Example: "The team members were aligned based on the project's objectives to ensure everyone was working towards the same goals."
Alternatives: "coordinated according to the" or "organized based on the".
The DNA sequences were aligned based on the protein alignment.
Protein-coding DNA sequences (CDS) were aligned based on the protein alignments in the DAMBE with the default parameters, then converted the CDS alignments into PAML format for further analyses [ 67, 68].
Thereafter, the nucleotide sequences were aligned based on the protein sequence alignment profile using PAL2NAL [ 61].
Prank [ 80] was used to conduct codon alignment, in which two protein sequences were aligned first and then DNA sequences were aligned based on the corresponding protein alignments.
A nucleotide alignment, which was used for the phylogenetic analysis, was aligned based on the deduced amino acid sequences using Clustal W. A general time reversible model with invariable sites and a gamma distribution for variable rate sites (GTR+I+G) was used.
The remainder of the sequences is then aligned based on the consistency constraints given by these pre-aligned positions.
The corresponding nucleotide sequences for these protein-coding genes were aligned based on indels inferred from the protein alignment; the web-based tool RevTrans [ 57], was used to place the indels in the nucleotide sequences.
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 protein-coding DNA sequences were aligned based on their protein alignments at the web server http://www.bork.embl.de/pal2nal/[ 27].
Furthermore, the genes were aligned based on gene orientation and to the species with the highest number of genes similar to DNA sequence alignments with indels.
(A, B ) YFP-Spc42-mTurquoise2 (SLJ9442) cells were arrested in α-factor and imaged by SIM. 17 images of the SPB (arrowhead) and satellite were aligned based on mTurquoise2 fluorescence to create the projection view shown in A. Bar, 200 nm.
