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. Jay
-----Original Message----- From: methods-boun...@oat.bio.indiana.edu [mailto:methods-boun...@oat.bio.indiana.edu] On Behalf Of Elyaseen Daniel Sent: Friday, May 18, 2012 5:43 AM To: meth...@magpie.bio.indiana.edu Subject: DNA sequence alignment Dear listers, Hello! 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. Elya _______________________________________________ Methods mailing list Methods@net.bio.net http://www.bio.net/biomail/listinfo/methods This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. _______________________________________________ Methods mailing list Methods@net.bio.net http://www.bio.net/biomail/listinfo/methods
