DNA sequence alignment

[Elyaseen Daniel]

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