multiple sequence alignment

Hello Oumed.

You can find most answers to your questions in the jalview manual which can be downloaded from the help and documentation pages on

Feel free to email the list again if you don’t find out what you want to know.

Hope this helps!
Jim Procter.


Sent from my android device.

-----Original Message-----
From: Oumed Gergis
To: “
Sent: Thu, 01 Aug 2013 10:34 AM
Subject: [Jalview-discuss] multiple sequence alignment

Dear Sir,

Thanks alot.

My questions are:

1.Is it mandatory to align equal sized sequences when aligning them or it is possible to align short with full length sequences?

2.Does deleting gaps affects the aligned sequences?

3.How to know the gap or residue is due to artifact?

4.How to know the quality of the alignment?

5.How to measure identity % distances among different sequences?example see table1 page 2455.

Best Regards