DNA sequence alignment

Jayakumar, R via methods%40net.bio.net (by R.Jayakumar from roswellpark.org)
Fri May 18 11:23:42 EST 2012

Try using Philip software for the phylogeny.  I have used this along with ClustatW for several years now and always gives expected results relative to the alignment.  It just might be the algorithm used by mega5 weights the pairing differently from what we visualize from an alignment.

-----Original Message-----
From: methods-bounces from oat.bio.indiana.edu [mailto:methods-bounces from oat.bio.indiana.edu] On Behalf Of Elyaseen Daniel
Sent: Friday, May 18, 2012 5:43 AM
To: methods from magpie.bio.indiana.edu
Subject: DNA sequence alignment

Dear listers,


I have sequnced a DNA fargment (PCR product) then BLASTed the sequnce (in NCBI BLAST). I got 97% similarity with a named species. I took my sequence and the six closest sequences and aligned them (Clustal W) then conducted a phylogeny analysis using MEGA 5 (using Neighbour-Joining with p-distance). The tree showed that my sequence is far from the one with 97% similarity (a really far clade!). If I do not align the sequences and run the same phylogeny analysis I get my sequence and the one with 97% similarity in ONE clade supported by a high bootstrap value (86%). Any explanations on why the alignment is making this change. (by the way I tried alignment with MUSCLE or doing Maximum Likelihood but that did not slove the problem). 

Thanks a mellion.

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