Distance Matrix

Hi,
  Is there a way to extract a sequence identity based distance matrix from a sequence alignment? Thanks.

Reza

Hi There, Reza.

The short answer is no - which is the same answer I gave in this thread:
http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/2010-June/000403.html

However, the reason the answer is no is because there isn't a GUI command to view or output the matrix, even though Jalview does include routines to calculate sequence similarity matrices. Jalview used to output a similarity matrix when it calculated a tree, and that could be re-instated really easily, but its not in any standard format, and we didn't think anyone used it - since most phylogenetic programs include a sequence distance-matrix calculation step as standard.

Could you give me an idea of what you want to use the matrix for ? Either email the list or post directly to the feature request I've created in the Jalview bug tracker here: http://issues.jalview.org/browse/JAL-547

Jim.

···

On 13/07/2010 12:41, Reza Khayat wrote:

Hi,
  Is there a way to extract a sequence identity based distance matrix
from a sequence alignment? Thanks.

Reza

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