The phrase "alignment analyses were" is correct and usable in written English.
It can be used in contexts discussing research, data evaluation, or methodologies where alignment analyses are being referenced.
Example: "The results of the alignment analyses were significant in determining the evolutionary relationships among the species."
Alternatives: "alignment assessments were" or "alignment evaluations were".
Multiple sequence alignment analyses were performed using ClustalX (version 1.83) program.
Multiple alignment analyses were performed using MUSCLE (version 3.6) program [ 85].
The GUIDANCE alignment analyses were conducted using the MAFFT algorithm and 100 bootstrap replicates, with variable amino acid position columns identified using the GUIDANCE method and then removed based on a column-score cutoff of <0.93.
DNA alignment analyses were conducted by using ClustalW version 1.83 (www.ebi.ac.uk/clustalw), and nucleotide substitutions were identified by using BioEdit version 7.0.1 (Isis Pharmaceuticals, Inc., Carlsbad, CA, USA) (7 ).
A striking result of the alignment analyses is that the H-Y-E catalytic site motif is fully conserved only in subgroups 1 and 2 (pARTs 1 6).
Multiple sequence alignment analyses are based largely on the assumptions that evolutionarily-conserved amino acids are more likely to be functionally important than nonconserved amino acids and substitutions involving chemically similar amino acids are less likely to be damaging than substitutions involving chemically different amino acids.
After alignment, phylogenetic analyses were conducted by using maximum-likelihood and Bayesian methods (1, 2 ).
Sequence alignment and analyses were performed online using the BLAST program available at the National Center for Biotechnology Information web page http://www.ncbi.nlm.nih.gov.nih.gov
Gene alignments and analyses were performed using Geneious Pro 5.0.3.
Sequence alignments and analyses were performed online using the BLAST program (http://www.ncbi.nlm.nih.gov/).nih.gov/
Alignments and analyses were computationally intensive, requiring several months on 18 fast processors.
