#! /bin/sh##  iterate_rates  file_name_root  program_options  [cycles]if test $# -lt 2; then    echo "Usage: iterate_rates  file_name_root  [cycles]";    exitfiroot0="$1"if   test -f "${root0}.phylip"; then suf=phylipelit test -f "${root0}.phy";    then suf=phyelse    echo "Could not find sequence file ${root0}.phy[lip]"    exitfiroot=`echo "$root0" | sed 's&^.*/\([^/][^/]*\)$&\1&'`if test $# -gt 2; then cycles=$3; else cycles=0; fitree1=`ls -1 ${root}_*.tree | tail -1`if test -z "$tree1"; then    transition 2 < ${root}.$suf | treefile | quickadd | global 0 0 | fastDNAml >/dev/null    mv `ls -t treefile.*|head -1`  "${root}.dummy_tree"    usertree  "${root}.dummy_tree" < ${root0}.$suf | n_categories 35 | treefile | DNAml_rates > /dev/null    mv `ls -t treefile.*|head -1`    v0=0;    v1=1;else    v0=`echo "$tree1" | sed 's/^.*_\([0-9][0-9]*)\.tree$/\1/'`    v1=`expr $v0 + 1`fiif test ! -f ${root}_${v0}.$suf; then ln -s ${root}.$suf ${root}_${v0}.$suf; fiusertree  $tree1 < ${root}_${v0}.$suf | n_categories 35 | treefile | frequencies | DNAml_rates > ${root}_${v0}.ratesmv  weight_rate.*  ${root}_${v0}.wrif test ! -f ${root}_${v1}.$suf; then ln -s ${root}.$suf ${root}_${v1}.$suf; fifastDNAml_loop -m 20 ${root}_${v1}.$suf 3 "frequencies | weights_categories ${root}_${v0}.wr"