CHAPTER 11Sequence Alignment Using Online Tools

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana


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:

  1. Color INteractive Editor for Multiple Alignments (CINEMA 2.1). CINEMA ( is freely available online. The sequence alignment is supported with a color editor.
  2. Multiple Alignment Construction and Analysis Workbench (MACAW) (‐ This is downloadable software that is used to identify localized sequence similarities and edits blocks of multiple sequences.
  3. Java ALignment VIEWer (JALVIEW) ( JALVIEW has freely accessible multiple alignment editors. Alignment tools like “EBI ClustalW” and protein domain database “Pfam” use this Java‐based platform.
  4. Clustal W ( Used for pairwise and multiple sequence alignment.
  5. Clustal Omega ( Clustal Omega is capable of handling several thousands of medium‐to‐large sized sequences simultaneously (Sievers and Higgins, 2014).
  6. Multiple Alignment using Fast Fourier Transform (MAFFT version 6) ( The multiple sequence alignment program MAFFT is available in both online and downloadable ...

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