Multiple sequence alignment (MSA), whether peptide or nucleotide, can be stored in multiple formats, most commonly Clustal’s .aln format or the FASTA format. While these files are plain text files, and can be opened and edited in any text editor, performing many of the tasks common to MSA analysis in such editors is unintuitive and time consuming. As identifying the mutatome of a quickly propagating virus species requires frequent and rapid identification of mutated sites, use of specialized software is crucial.
Two examples of software we use to analyze aligned FASTA files are Jalview and UGene, the former for customizable image generation, the latter for ease of export for specific sites, such as variant nucleotides compared to reference sequences, or gap regions. A quick overview of basic use of these software can be helpful for researchers less familiar with such analyses.
The following researches have contributed to the content above, listed alphabetically in order of surname:
ESKİER, Doğa
KARAKÜLAH, Gökhan, PhD