The phrase "alignment was used for" is correct and usable in written English.
It can be used when explaining the purpose or application of alignment in a specific context, such as in a project or study.
Example: "In our research, alignment was used for ensuring that all team members were on the same page regarding project goals."
Alternatives: "alignment served to" or "alignment was applied for".
Next, predicted amino acid sequences of 25 fungal Nbs1 orthologs identified by PSI-BLASTp from Genbank were aligned by ClustalX (Chenna et al. 2003), and this alignment was used for a more thorough and sensitive search of the C. cinereus genome by PSI-BLASTp using a custom position-specific scoring matrix (PSSM).
Sixteen metagenomic MCP sequences were aligned with the MCP sequences from complete virophage genomes, and the resulting multiple alignment was used for phylogenetic tree construction.
Alignment adjustment using Gblocks, which eliminates poorly aligned positions and divergent regions, resulted in few changes; therefore, the original, unadjusted alignment was used for the construction of phylogenetic trees.
Where appropriate, a longer alignment was used for the phylogenetic analysis (see supplementary data).
For phylogenetic analyses, a 582-bp region of the sequence alignment was used for amoA and a 1272-bp region for 16S rRNA.
This alignment was used for recombinant sequence screening (Fig 1) and generation of phylogenetic trees for different regions of the cap gene (Fig 2) as described in Materials and Methods.
A permutation alignment is used for grouping each extracted signal into the correct source output before transforming them into the time domain.
Only gap-free conserved regions of the alignment were used for the construction of the tree (164 amino acid positions).
Alignment seeds are generated by streaming reads against the reference suffix tree, and then Smith Waterman alignment is used for tuning.
Because this bias is not adequately addressed by amino acid substitution models and due to the short length of the alignment, both the amino acid and corresponding nucleotide alignment were used for phylogenetic analysis.
