＜このページは未完成です＞
PAUP*をWindowsで使うときに便利なPAUPブロックまとめました。NEXUSファイルにコピーペーストして使ってください。
~目次~
#contents

*Maximum Parsimony [#sdd56ed1]
**Parsimony 一般 [#yae69673]
 Begin PAUP;
 set autoclose=yes warnreset=no increase=auto; [This turns off all user-prompts.]
 set criterion = parsimony; [This specifies the parsimony method]
 HSearch ;[BandBやAllTreesが使える]
 SaveTrees BrLens=yes File=MyFile.tre replace = yes;  [Saves the trees including branch lengths to the file named MyFile.tre]
 End;
**Heuristic Search [#c06ea5e1]
 begin PAUP;
 log file=Hsearch.log;
 set autoclose=yes;
 hsearch start=stepwise addseq=random nreps=100 savereps=yes randomize=addseq rstatus=yes hold=1 swap=tbr multrees=yes;
 savetrees file=Hsearch_all.tre;
 filter best=yes permdel=yes;
 savetrees file=Hsearch_best.tre;
 log stop;
 end;

**Bootstrap Search by Heuristic[#f1043305]
 begin PAUP;
 log start = yes file = MyBoot.log replace = yes;
 Bootstrap search = heuristic  nreps = 100 conLevel = 50;
 saveTrees from = 1 to=1 file=MyBoot.tre saveBootP=nodeLabels maxDecimals=1 replace=yes;
 log stop;
 end;

~　別にセーブしたTreeFileから読み込んで使うなら、このブロックと次のブロック。~
 begin paup;
 gettrees allblocks=yes duptrees=keep storetreewts=yes mode=7 file=Bootstrap.tre;
 end;

~　次に~
 begin paup;
 log file=bootstrapconsensus.log;
 contree /majrule=yes strict=no le50=yes usetreewts=yes showtree=yes treefile=Final_bootstrap.tre grpfreq=yes;
 log stop;
 end;

**ILD Test (Partition Homogeneity Test) [#i420d7a1]
 Begin PAUP;
 log file=ILDtest.log;
 hompart partition=[name] nreps=100 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq rstatus=no hold=1 swap=tbr multrees=yes;
 log stop;
 end ;

*Maximum Likelihood [#w20a850b]
** ML for Coding region [#f38ddf4b]
 begin paup;
 set autoclose=yes warnreset=no increase=auto;
 charset first = 1-.\3; [￥はPAUP上では＼（バックスラッシュ）]
 charset second = 2-.\3;
 charset third = 3-.\3;
 charpartition by_codon = 1:first,2:second,3:third;
 set criterion=parsimony; 
 hsearch;
 set criterion=likelihood;
 lset nst=6 rmatrix=estimate basefreq=estimate rates=sitespec siterates=partition:by_codon;
 lscores 1;
 lset rmatrix=prev basefreq=prev rates = sitespec   siterates = prev;
   hsearch start=1;
 savetrees brlens=yes maxDecimals=4 file=ML_out.tre replace=yes;
 end;

** ML for Coding region Modeltest用（但し簡便法） [#ve7c369a]
 begin paup;
 set autoclose=yes warnreset=no increase=auto;
 charset first = 1-.\3; 
 charset second = 2-.\3;
 charset third = 3-.\3;
 charpartition by_codon = 1:first,2:second,3:third;
 set criterion=parsimony; 
 hsearch;
 set criterion=likelihood;
 [ここにModeltestの結果のLsetから始まる行をはりつけるが、その行に
 rates=sitespec siterates=partition:by_codonを追加する。Modeltestの
 結果にratesとsiteratesがあれば削除。]
  hsearch start=1;
 savetrees brlens=yes maxDecimals=4 file=ML_out.tre replace=yes;
 end;

** ML for Non Coding region [#u91162a8]
 begin paup;
 set autoclose=yes warnreset=no increase=auto;
 set criterion=parsimony; 
 hsearch;
 set criterion=likelihood;
 lset nst=6 rmatrix=estimate basefreq=estimate rates=gamma shape = estimate;
 lscores 1;
 lset rmatrix=prev basefreq=prev rates = prev   shape = prev;
 hsearch start=1;
 savetrees brlens=yes maxDecimals=4 file=ML_out.tre replace=yes;
 end;

** ML for Non Coding region  Modeltest 用[#yddd035b]
 begin paup;
 set autoclose=yes warnreset=no increase=auto;
 set criterion=parsimony; 
 hsearch;
 set criterion=likelihood;
 [ここにModeltestの結果のLsetから始まる行を挿入]
 hsearch start=1;
 savetrees brlens=yes maxDecimals=4 file=ML_out.tre replace=yes;
 end;

*NJ[#u503d4ad]
** NJでBootstrap [#s572c8c9]
 Begin PAUP;
 log start = yes file = MyFile.log replace = yes;
 set criterion=distance;
 Bootstrap search = NJ  nreps = 100 conLevel = 50;
 saveTrees from = 1 to=1 file=NJ_boot.tre saveBootP=nodeLabels maxDecimals=1 replace=yes;
 end;