Subsitution Matricies

zharkikh at HGC6.SPH.UTH.TMC.EDU zharkikh at HGC6.SPH.UTH.TMC.EDU
Fri Oct 6 09:38:08 EST 1995

Jeff Huckaby asks:

To anyone who can help.....

        I have aligned several transposase sequences using CLUSTALW, but  
I am unsure as to what matrix is appropriate for determing homology  
between these transposase sequences.   
Any suggestions would be useful....



if the phylogeny of transposases is "clear-cut", you can apply
almost any distance measure (Jukes-Cantor, Kimura, PAM, ...)
to resolve it. As these are coding sequences, the most appropriate
would be using a measure that distinguish between synonymous and
nonsynonymous substitutions (I hope you have DNA/RNA sequences,
not amino acid). For this purpose, I suggest the Li's (1993) method
implemented in his LWL program. The Unix and DOS versions of the program
can be found at


under name "matdisli.c". Its combination with the Neighbor-Joining
method is given in the program "njbootli.c".
All these can be also retrieved from anonymous FTP site at




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