[PAUP* block to make a NJ phylogenetic tree]
BEGIN PAUP;
log file=***.nj.log;
set autoclose=no criterion=distance notifybeep=yes;
dset distance=hky85;
NJ;
savetrees format=nexus brlens=yes append=yes file=***.nj.nex;
lscores 1/scorefile=***.nj.sf append=yes;
bootstrap search=nj nreps=1000;
END;

[ Version 2.0 (29 July 2005) ]
[ This file written by Bevan Weir ]
[ downloaded from http://www.rhizobia.co.nz ]
[ Replace "*" above with your gene name ]
[ Every line must end with a " ; " ]