Mafft mismatch value

Medhat · 01-12-2016, 01:19 AM

Hi,

I tried to find both in
http://mafft.cbrc.jp/alignment/softw...al/manual.html
and
http://mafft.cbrc.jp/alignment/softw...lgorithms.html

to find the nucleotide mismatch value that mafft uses but I could not find it,

Any idea what is the value?

knowing that
Scoring matrix for nucleotide alignment. The default scoring matrix is derived from Kimura's two-parameter model. The ratio of transitions to transversions is set at 2 by default. Other parameters can be used, but have not yet been tested.

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01-12-2016, 01:19 AM	#1
Medhat Member Location: Poland Join Date: Jun 2013 Posts: 37	Mafft mismatch value Hi, I tried to find both in http://mafft.cbrc.jp/alignment/softw...al/manual.html and http://mafft.cbrc.jp/alignment/softw...lgorithms.html to find the nucleotide mismatch value that mafft uses but I could not find it, Any idea what is the value? knowing that Scoring matrix for nucleotide alignment. The default scoring matrix is derived from Kimura's two-parameter model. The ratio of transitions to transversions is set at 2 by default. Other parameters can be used, but have not yet been tested.