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outgroup 56 57;

bootstrap nreps=1000 conlevel=50 treefile=bootstrap.tre keepall=yes cutoffpct=50/start=stepwise addseq=random nreps=100 savereps=yes nchuck=20 chuckscore=5 dstatus=none; log stop; end;

附录 5. Paup运行ML分析

苹果机： BEGIN PAUP;

Lset Base=(0.3271 0.1847 0.1967) Nst=6 Rmat=(0.9731 1.0473 0.2212 0.4660 1.5241) Rates=gamma Shape=0.8160 Pinvar=0.6410; END; PC机： Begin Paup;

Set criterion=likelihood;

Lset Base=(0.3413 0.2847 0.0895) Nst=6 Rmat=(0.3885 3.5246 0.5305 0.4364 3.2970) Rates=gamma Shape=0.5232 Pinvar=0.2613; Hsearch start=nj nchuck=2 chuckscore=5 dstatus=none; savetrees format=nexus brlens=yes append=yes file=likelihood; lscores 1/scorefile=likelihood.sf append=yes;

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set root=outgroup; outgroup 27 28; showtrees all; end;

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