[Bio-software] Clustal percent identity matrix

[arun iyer]

I was wondering if the % identity matrix in clustal is actually useful to assign an bacteria as a distinct species. 
I ran an multiple alignment for DNA using default parameters. the % identity matrix shows that the 2 organisms is 97% identical. The absoulute nucleotide identity is 99%. 
the % ID matrix is generated after penalties...but is it really useful?


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