How to select representative sequence from multiple sequence alignment

[charlesxu90]

Hi all,

I'm working on a project which needs to find a representative sequence from multiple sequence alignment result (from clustalw).

My problem is like this:

This are aligned sequences:
ATCGACGTAC
A-CGA-GTAG
A-CGA-CTAC
A-CGA-GTAC

This is what I want:
ACGAGTAC

Which returns the mode of each base. If the mode of a base is a gap, then return the gap.

[TiborNagy]

You can use showalign from the Emboss package to get consensus sequence.

[charlesxu90]

You can use showalign from the Emboss package to get consensus sequence.

I tried but couldn't install Emboss package. It might be out of date, and cannot be downloaded now.

[GenoMax]

I tried but couldn't install Emboss package. It might be out of date, and cannot be downloaded now.

Did you try to download from this site: ftp://emboss.open-bio.org/pub/EMBOSS/
Latest version is 6.6.0 released July 2013.

[charlesxu90]

Did you try to download from this site: ftp://emboss.open-bio.org/pub/EMBOSS/
Latest version is 6.6.0 released July 2013.

It works. Thank you.