The phrase "alignments were analyzed by" is correct and usable in written English.
It can be used in contexts where you are describing a process of examining or studying alignments, often in research or data analysis.
Example: "In our study, the alignments were analyzed by comparing the sequences to identify similarities and differences."
Alternatives: "alignments were examined by" or "alignments were assessed by".
Sequences were aligned to corresponding HMM by using HMMALIGN and the resulting alignments were analyzed by RNAz (version 0.1.1) [ 37].
The nucleotide sequence alignments were analyzed by using MRBAYES 3.1.2 (12 ) in the computer software package PAUP*, version 4.0b10 (http://paup.csit.fsu.edu).
The TopHat alignments were analyzed by coverageBed (BEDTools v.2.16.2 [ 48] to count the number of reads per genome base location.
Abnormal paired-end alignments were analyzed by clustering and comparing with the types of structure variation previously defined using the software Breakdancer [ 20] run using the default parameters.
Other than the template alignment (32 taxa, 318 positions), which was analyzed by ML and ML-corrected distance only, all alignments were analyzed by all three methods.
In order to identify allelic polymorphs, nucleotide alignments were analyzed by eye and two sequences were considered as alleles, when, with the exception of a few polymorphic changes at third codon positions, large stretches of the compared sequences were identical.
DGAT1 from selected species were from NCBI and homology alignment was analyzed by ClustalX2.
Each alignment was analyzed by Maximum Parsimony (MP), Neighbour Joining (NJ) and Maximum Likelihood (ML) using PAUP 4.0b10 [50].
The same alignment was analyzed by GARD program available at the datamonkey server using HKY85 substitution model.
The resulting alignment was analyzed by using Bayesian methods of phylogenetic reconstruction and the GTR+Γ evolutionary model.
The PpMIP sequence alignment was analyzed by three different phylogenetic methods, Neighbour Joining (NJ), Maximum Parsimony (MP) and Bayesian inference (Bay).
