Dear Anderson Amorim ,

I think your best chance is to use an online version of the tool:

https://www.ebi.ac.uk/Tools/msa/kalign/

If you want an offline Windows compatible tool for multiple alignments and don't mind using something else than Kalign, I think MEGA can get the job done rather nicely:

https://www.megasoftware.net/

Good luck,

Gautier

The Kalign program and a Kalign server are freely available at http://msa.cgb.ki.se

Kalign is a fast and robust alignment method. It is especially well suited for the increasingly important task of aligning large numbers of sequences. In terms of computational efficiency, Kalign is superior to the other methods, and readily aligns hundreds of sequences in minutes on a normal desktop computer. Coupled with the fact that Kalign gives very accurate alignments, this makes Kalign a very attractive overall method.

Dear colleagues, thank you for your answers!

I know the online interface to run Kalign.

Actually, I'm developing a Windows interface tool, that in a moment of its execution, I need to run Kalign. To reach a better performance, it would be great to call just the executable file through a command line.

I'm gonna try to compile the Unix code on Windows environment and see how it works.

Thank you all, again.

Regards.

Get cygwin (https://www.cygwin.com/) installed on your windows box and see if it works. The libraries are extensive and I've yet to run into a program that didn't run on cygwin.

Hi Anderson,

I found a Windows version of kalign.exe file here:

ftp://ftp.ncbi.nlm.nih.gov/toolbox/gbench/kalign/

I have a similar need. My C# program calls Kalign repeated to align each intermediate data set. It works pretty well.

Good luck!

Thanks a lot, Dr. Spencer!

Regards.