# enshu200209/memo200209.txt

# create enshu directory
cmd001

# prepare data files in "data" directory

# setup data {catgb|nucgb|lstgb|namegb}.txt
cmd101

# edit namegb.txt

# setup work-*.nsq (nuc sequence data in FASTA format)
cmd121

# setup work-*.psq (ptn sequence data in FASTA format)
cmd141

# run clustalw
cmd201

# convert *.aln to *.ptn
cmd221

# conc *.ptn 
cmd241

# molphy nj analysis
cmd311

# molphy local ml analysis
cmd331

# make constraint tree
  work-conc-clade.txt
  work-conc-constraint.tpl
  repnamegb -p 2 work-conc-clade.txt > work-conc-clade-name.txt

# molphy approx ml analysis
cmd351

# edit user tree
  cp work-conc-user.tpl work-conc-user-orig.tpl
  work-conc-user.tpl

# molphy usertree ml analysis
cmd371

# make bootstrap replicates
cmd411

# calculate p-values for trees
cmd431

# calculate p-values for edges
cmd451

# edit work-conc-ass.log
  work-conc-tree-list1.txt
  repnamegb -sv -p 4 -l work-conc-clade.txt work-conc-tree-list1.txt > work-conc-tree-list2.txt
  work-conc-edge-list1.txt
  work-conc-edge-list2.txt

# sort trees and edges according to AU p-value
  sortlines -c 3 -f work-conc-tree.log work-conc-tree-list2.txt > work-conc-tree-sort.txt
  sortlines -c 3 -f work-conc-edge.log work-conc-edge-list2.txt > work-conc-edge-sort.txt

# edit 
  work-conc-tree-sum.txt
  work-conc-edge-sum.txt

# copy the result
  cp namegb.txt result
  cp lstgb.txt result
  cp work-conc-tree-sum.txt result
  cp work-conc-edge-sum.txt result
  cp work-conc-clade.txt result
  cp work-conc-clade-name.txt result
  cp work-conc-nj-name.eps result
  cp work-conc-ml-name.eps result
  cp work-conc-user-name.eps result