Anyone Use Normd As A Quality Control For Msas

Question

[Will]

I'm trying to use a method for finding poorly aligned sequences. I found this question: Automagically remove “badly” aligning sequence from Multiple-Sequence Alignment. Which led me to the NorMD paper which supposedly has code at ftp://ftp-igbmc.u-strasbg.fr/pub/NORMD/ ... The paper is still being cited as recently as 2010 so someone still has to have the code around somewhere.

I haven't been able to find their code. Does anyone have any suggestions ... besides re-coding it myself.

Answer 1

[Pierre Lindenbaum]

Hu? The C source code is available in the FTP site you mentioned.

[Michael Schubert]

Confirming the Chrome error.

[Will]

That's super strange ... I get a 404 error when trying to access that web-address.

[Pierre Lindenbaum]

What's your email ? I can send you this tar.gz if you want.

[Will]

must be a Chrome thing ... opening in firefox fixed it. ... thanks for the quick response Pierre.

[Steve Moss]

I was just looking for this too, and managed to find norMD1_3.tar.gz after searching Google, however, the version I have, when compiled, returns:

./normd Version 1.2

Is this the same with your version Pierre? I wondered if they just hadn't incremented the version number in the source?

[Steve Moss]

The README has the following, so I assume it must be the latter?

norMD Objective Function for multiple sequence alignments
                (version 1.3, Jan 2003)