It is currently Mon Jun 17, 2019 9:01 am



Reply to topic  [ 1 post ] 
Clustering an alignment based on phylogenetic trees 
Author Message
User avatar

Joined: Thu Dec 07, 2006 6:20 pm
Posts: 173
Location: Cambridge, UK
Post Clustering an alignment based on phylogenetic trees
If you want to cluster an alignment according to the similarity of the sequences you can use a phylogenetic reconstruction to do this.

First you need to align DNA and/or Protein sequences using ClustalW as an automatic algorithm. At this point you can then edit alignments manually if you wish. Then to cluster the sequences run a phylogenetic reconstruction on them.
Code:
ANALYZE > CONSTRUCT TREE


From the resulting phylogenetic window, you can rearrange sequences if necessary by selecting nodes and "rotating" them with the toolbar buttons. Finally, with the focus on the Phylogeny window sort the alignment to match the tree

Code:
ANALYZE > PHYLOGENETIC ANALYSES > SORT MSA TO MATCH TREE


This will rearrange the sequences in the editor to match the phylogeny branches.


Mon Sep 15, 2008 10:26 pm
Profile WWW
Display posts from previous:  Sort by  
Reply to topic   [ 1 post ] 

Who is online

Users browsing this forum: No registered users and 2 guests


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Jump to:  
cron
Powered by phpBB © 2000, 2002, 2005, 2007 phpBB Group.
Designed by ST Software for PTF.