请问如何使用paup执行Shimodaira－Hasegawa检验？急用！谢谢指点！

Shimodaira－Hasegawa一般是用来检测不同的序列能否联合分析，分子钟检测用Likelihood Ratio Test (LRT),如下命令集：(其中的模式参数他外类群根据你自己的数据作修改)

BEGIN PAUP;
set criterion=distance;
log file=Time_clocktest.log;
DSet distance=JC objective=ME base=equal rates=equal pinv=0
subst=all negbrlen=setzero;
NJ showtree=no breakties=random;
set criterion=likelihood;
lset clock=no;
Lscores 1/ Base=(0.3513 0.1639 0.1691) Nst=6 Rmat=(0.8425 1.3814 0.3935 0.8474 1.5819) Rates=gamma Shape=1.7738 Pinvar=0.1525
clock=no scorefile=Time_clocktest.scores append=yes;[LSCORES];
;[!Non-clock score above, clock score below];
roottrees;
outgroup Solanum_p Rubia_fru;
lset clock=yes;
Lscores 1/ Base=(0.3513 0.1639 0.1691) Nst=6 Rmat=(0.8425 1.3814 0.3935 0.8474 1.5819) Rates=gamma Shape=1.7738 Pinvar=0.1525
scorefile=Time_clocktest.scores append=yes;[LSCORES];
;[!Clock score above];
tstatus;
log stop;
end;