Algorithms used to do pairwise or multiple sequence alignments vary with the sequence alignment tool available online. Links to some useful sites for sequence alignment are given below:
- Color INteractive Editor for Multiple Alignments (CINEMA 2.1). CINEMA (http://www.bioinf.man.ac.uk/dbbrowser/CINEMA2.1/) is freely available online. The sequence alignment is supported with a color editor.
- Multiple Alignment Construction and Analysis Workbench (MACAW) (http://en.bio‐soft.net/format/MACAW.html). This is downloadable software that is used to identify localized sequence similarities and edits blocks of multiple sequences.
- Java ALignment VIEWer (JALVIEW) (http://www.jalview.org/). JALVIEW has freely accessible multiple alignment editors. Alignment tools like “EBI ClustalW” and protein domain database “Pfam” use this Java‐based platform.
- Clustal W (http://www.ebi.ac.uk/Tools/clustalw2/index.html). Used for pairwise and multiple sequence alignment.
- Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/). Clustal Omega is capable of handling several thousands of medium‐to‐large sized sequences simultaneously (Sievers and Higgins, 2014).
- Multiple Alignment using Fast Fourier Transform (MAFFT version 6) (http://mafft.cbrc.jp/alignment/software/index.html). The multiple sequence alignment program MAFFT is available in both online and downloadable ...