ae2dnaml

fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memo

#! /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