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|
#! /bin/sh
#
# ae2dnaml ae2_file_name [ "dnaml_opt1 | dnaml_opt2 | ..." ]
#
temp_file="$1.$$.phy"
stdopt="quickadd | treefile | frequencies"
if test $# -eq 1; then
opts=$stdopt;
elif test $# -eq 2; then
if test -n "$2"; then opts="$stdopt | $2"
else opts="$stdopt"
fi
else
comm=`echo $0 | sed -e 's&^.*/&&g'`
optprm="[ "'"'"dnaml_opt1 [ | dnaml_opt2 [...]]"'"'" ]"
echo "
Usage: $comm ae2_file $optprm
Quickadd, frequencies and treefile are included by the script and should
not be specified by the user. Additional fastDNAml program options are
enclosed in quotes, and separated by vertical bars (|).
"
exit
fi
convp -ae2 "$1" -phylip "$temp_file"
echo "Working on tree"
id=`eval "cat < $temp_file | $opts | out.PID -o $1 fastDNAml"`
rm -f "$temp_file" checkpoint.$id
mv treefile.$id $1.tree
#treetool2 $1.tree
|
