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