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附录1.最大简约法分析批处理文件

1.

begin PAUP;

log file=hsearch1.log; set autoclose=yes;

set maxtrees=100 increase=auto;

hsearch start=stepwise addseq=random nreps=1000 randomize=addseq

rstatus=yes

hold=1

swap=tbr

nchuck=200 chuckscore=1;

savetrees file=hsearch1.all.tre brlens=yes; filter best=yes permdel=yes; savetrees file=hsearch1.best.tre; gettrees file=hsearch1.best.tre;

contree all/majrule=yes treefile=contree.tre; log stop; end; 2.

begin PAUP;

log file=hsearch1.log; set autoclose=yes;

set maxtrees=100 increase=auto;

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savereps=yes multrees=yes

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hsearch start=stepwise addseq=random nreps=1000 savereps=yes randomize=addseq rstatus=yes hold=1 swap=tbr multrees=yes; savetrees file=hsearch1.all.tre brlens=yes; filter best=yes permdel=yes; savetrees file=hsearch1.best.tre; gettrees file=hsearch1.best.tre;

contree all/majrule=yes treefile=contree.tre; log stop; end;

2的策略较好，是hsearch中首选，而如果此程序运算时间太长则用上面一个程序。

本实用方法只提供hsearch，而branch and bound和exhaustive方法省略。 附录1*

export format=nexus interleaved=no file=temp.txt （此为生成noninterleave文件命令）

附录 2. ILD分析

;

endblock;

charpartition dna=ITS:1-848,trnLF:849-3051; begin paup;

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set criterion=parsimony; log file=iscap.hom;

hompart part=dna nreps=100/addseq=random; hsearch swap=tbr; endblock;

附录 3. Bayes分析

1. 单一模型 begin mrbayes;

lset nst=6 rates=gamma;

mcmcp ngen=2000000 printfreq=1000 samplefreq=100 savebrlens=yes filename=P_combined; mcmc;

sumt filename=P_combined.t burnin=2000; end;

Begin mrbayes;

2. 多模型 begin mrbayes; charset its=1-622; charset trnlf=623-1696; charset matk=1697-3221;

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charset chs=3222-4406; charset psbm2trnd=4407-5506; charset psbm=5507-6279; charset gpd=6280-6972; charset LFY=6973-8426;

partition Names = 8: its, trnlf, matk, chs, psbm2trnd, psbm, gpd, LFY; end;

begin mrbayes;

[The following lines set up a model in which all four genes have their

unique GTR + gamma

+ propinv model] set partition=Names; prset ratepr=variable;

lset applyto=(1,2,3,4,5,6,7) nst=6;

lset applyto=(8) nst=2 rates=gamma;

unlink shape=(all) pinvar=(all);

end;

begin mrbayes;

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mcmcp ngen=100000 printfreq=1000 samplefreq=100 nchains=4 savebrlens=yes filename=solms8mys; mcmc;

sumt filename=solms8.t burnin=3000; end;

3. 带支长contree的运算batch begin mrbayes;

log start filename=cp.log;

mcmc filename=cp ngen=2000000 samplefreq=100; sump

burnin=5000

filename=cp

outputname=cp.sump;

sumt burnin=5000 filename=cp contype=allcompat; log stop; end;

附录4. bootstrap分析

begin paup;

log file=bootstrap.log;

set maxtrees=100 increase=auto; set criterion=parsimony; set root=outgroup;

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printtofile=yes