Dear any,

I think there are a lot of different tools.

What format does your final file have?

There are some examples below:

java script multiple sequence alignment viewer

A: Ngs Reads Alignment

http://www.ormbunkar.se/aliview/

http://globin.bx.psu.edu/dist/gmaj/

I've used simple fasta-file alignments.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3454398/

see Materials and Methods and Figure 4 or some other figures as an example.

"Multiple alignments of protein and DNA sequences were constructed using

Muscle 3.6 (http://www.drive5.com/muscle/) [47] and visualized and manually edited using

GeneDoc Editor version 2.6.002 (http://www.nrbsc.org/gfx/genedoc/; Nicholas, Karl B and Nicholas, Hugh B. Jr. 1997,

• I updated the url below.

GeneDoc: a tool for editing and annotating multiple sequence alignments. Distributed by the authors).

https://www.psc.edu/index.php/user-resources/software/genedoc

http://en.freedownloadmanager.org/Windows-PC/GeneDoc-FREE.html