diff -r -u glimmer3.02.old/docs/notes.tex glimmer3.02/docs/notes.tex
--- glimmer3.02.old/docs/notes.tex	2006-06-12 21:40:14.000000000 +0200
+++ glimmer3.02/docs/notes.tex	2015-05-25 22:41:39.450340098 +0200
@@ -306,7 +306,7 @@
   The script would then run the commands:
 \BSV\begin{verbatim}
   long-orfs -n -t 1.15 genom.seq run1.longorfs
-  extract -t genom.seq run1.longorfs > run1.train
+  glimmer_extract -t genom.seq run1.longorfs > run1.train
   build-icm -r run1.icm < run1.train
   glimmer3 -o50 -g110 -t30 genom.seq run1.icm run1
 \end{verbatim}\ESV
@@ -330,9 +330,9 @@
 \end{verbatim}\ESV
   The script would then run the commands:
 \BSV\begin{verbatim}
-  extract -t genom.seq train.coords > run2.train
+  glimmer_extract -t genom.seq train.coords > run2.train
   build-icm -r run2.icm < run2.train
-  upstream-coords.awk 25 0 train.coords | extract genom.seq - > run2.upstream
+  upstream-coords.awk 25 0 train.coords | glimmer_extract genom.seq - > run2.upstream
   elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif
   set startuse = `start-codon-distrib -3 genom.seq train.coords`
   glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse genom.seq run2.icm run2
@@ -358,11 +358,11 @@
   The script would then run the commands:
 \BSV\begin{verbatim}
   long-orfs -n -t 1.15 genom.seq run3.longorfs
-  extract -t genom.seq run3.longorfs > run3.train
+  glimmer_extract -t genom.seq run3.longorfs > run3.train
   build-icm -r run3.icm < run3.train
   glimmer3 -o50 -g110 -t30 genom.seq run3.icm run3.run1
   tail +2 run3.run1.predict > run3.coords
-  upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream
+  upstream-coords.awk 25 0 run3.coords | glimmer_extract genom.seq - > run3.upstream
   elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif
   set startuse = `start-codon-distrib -3 genom.seq run3.coords`
   glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3
@@ -1081,12 +1081,12 @@
   \Pg{entropy-score}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
 \eq
 
-\subsubsection{\Pg{extract} Program}
+\subsubsection{\Pg{glimmer_extract} Program}
 This program reads a genome sequence and a list of coordinates
 for it and outputs a multi-fasta file of the regions specified
 by the coordinates.  Output goes to standard output.
 \bq
-  \Pg{extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
+  \Pg{glimmer_extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
 \eq
 
 \subsubsection{\Pg{multi-extract} Program}
diff -r -u glimmer3.02.old/sample-run/g3-from-scratch.csh glimmer3.02/sample-run/g3-from-scratch.csh
--- glimmer3.02.old/sample-run/g3-from-scratch.csh	2006-06-12 21:46:35.000000000 +0200
+++ glimmer3.02/sample-run/g3-from-scratch.csh	2015-05-25 22:40:18.450338748 +0200
@@ -50,7 +50,7 @@
 step2:
 # Extract the training sequences from the genome file
 echo "Step 2 of ${numsteps}:  Extracting training sequences"
-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
 if  ($status != 0)  then
   echo "Failed to extract training sequences"
   exit
diff -r -u glimmer3.02.old/sample-run/g3-from-training.csh glimmer3.02/sample-run/g3-from-training.csh
--- glimmer3.02.old/sample-run/g3-from-training.csh	2006-06-12 21:46:35.000000000 +0200
+++ glimmer3.02/sample-run/g3-from-training.csh	2015-05-25 22:40:18.450338748 +0200
@@ -42,7 +42,7 @@
 step1:
 # Extract the training sequences from the genome file
 echo "Step 1 of ${numsteps}:  Extracting training sequences"
-$glimmerpath/extract -t $genome $coords > $tag.train
+$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
 if  ($status != 0)  then
   echo "Failed to extract training sequences"
   exit
@@ -66,7 +66,7 @@
 # upstream of the start locations in $coords
 echo "Step 3 of ${numsteps}:  Making PWM from upstream regions"
 $awkpath/upstream-coords.awk 25 0 $coords \
-   | $glimmerpath/extract $genome - > $tag.upstream
+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
 $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
 if  ($status != 0)  then
   echo "Failed to create PWM"
diff -r -u glimmer3.02.old/sample-run/g3-iterated.csh glimmer3.02/sample-run/g3-iterated.csh
--- glimmer3.02.old/sample-run/g3-iterated.csh	2006-06-13 14:15:28.000000000 +0200
+++ glimmer3.02/sample-run/g3-iterated.csh	2015-05-25 22:40:18.450338748 +0200
@@ -57,7 +57,7 @@
 step2:
 # Extract the training sequences from the genome file
 echo "Step 2 of ${numsteps}:  Extracting training sequences"
-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
 if  ($status != 0)  then
   echo "Failed to extract training sequences"
   exit
@@ -103,7 +103,7 @@
 # upstream of the start locations in $tag.coords
 echo "Step 6 of ${numsteps}:  Making PWM from upstream regions"
 $awkpath/upstream-coords.awk 25 0 $tag.coords \
-   | $glimmerpath/extract $genome - > $tag.upstream
+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
 $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
 if  ($status != 0)  then
   echo "Failed to create PWM"
diff -r -u glimmer3.02.old/scripts/g3-from-scratch.csh glimmer3.02/scripts/g3-from-scratch.csh
--- glimmer3.02.old/scripts/g3-from-scratch.csh	2006-06-12 21:40:14.000000000 +0200
+++ glimmer3.02/scripts/g3-from-scratch.csh	2015-05-25 22:44:44.190343177 +0200
@@ -50,7 +50,7 @@
 step2:
 # Extract the training sequences from the genome file
 echo "Step 2 of ${numsteps}:  Extracting training sequences"
-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
 if  ($status != 0)  then
   echo "Failed to extract training sequences"
   exit
diff -r -u glimmer3.02.old/scripts/g3-from-training.csh glimmer3.02/scripts/g3-from-training.csh
--- glimmer3.02.old/scripts/g3-from-training.csh	2006-06-12 21:40:14.000000000 +0200
+++ glimmer3.02/scripts/g3-from-training.csh	2015-05-25 22:44:44.190343177 +0200
@@ -42,7 +42,7 @@
 step1:
 # Extract the training sequences from the genome file
 echo "Step 1 of ${numsteps}:  Extracting training sequences"
-$glimmerpath/extract -t $genome $coords > $tag.train
+$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
 if  ($status != 0)  then
   echo "Failed to extract training sequences"
   exit
@@ -66,7 +66,7 @@
 # upstream of the start locations in $coords
 echo "Step 3 of ${numsteps}:  Making PWM from upstream regions"
 $awkpath/upstream-coords.awk 25 0 $coords \
-   | $glimmerpath/extract $genome - > $tag.upstream
+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
 $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
 if  ($status != 0)  then
   echo "Failed to create PWM"
diff -r -u glimmer3.02.old/scripts/g3-iterated.csh glimmer3.02/scripts/g3-iterated.csh
--- glimmer3.02.old/scripts/g3-iterated.csh	2006-06-13 14:15:46.000000000 +0200
+++ glimmer3.02/scripts/g3-iterated.csh	2015-05-25 22:44:44.190343177 +0200
@@ -57,7 +57,7 @@
 step2:
 # Extract the training sequences from the genome file
 echo "Step 2 of ${numsteps}:  Extracting training sequences"
-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
 if  ($status != 0)  then
   echo "Failed to extract training sequences"
   exit
@@ -103,7 +103,7 @@
 # upstream of the start locations in $tag.coords
 echo "Step 6 of ${numsteps}:  Making PWM from upstream regions"
 $awkpath/upstream-coords.awk 25 0 $tag.coords \
-   | $glimmerpath/extract $genome - > $tag.upstream
+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
 $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
 if  ($status != 0)  then
   echo "Failed to create PWM"
diff -r -u glimmer3.02.old/src/Util/Makefile glimmer3.02/src/Util/Makefile
--- glimmer3.02.old/src/Util/Makefile	2006-06-12 21:40:14.000000000 +0200
+++ glimmer3.02/src/Util/Makefile	2015-05-25 22:43:12.760341653 +0200
@@ -8,7 +8,7 @@
 SOURCES = $(UTIL_SRCS)
 OBJECTS = $(UTIL_OBJS)
 
-PROGS = entropy-profile entropy-score extract multi-extract start-codon-distrib \
+PROGS = entropy-profile entropy-score glimmer_extract multi-extract start-codon-distrib \
   uncovered window-acgt
 
 LIBRARIES = 
diff -r -u glimmer3.02.old/src/Util/extract.cc glimmer3.02/src/Util/extract.cc
--- glimmer3.02.old/src/Util/extract.cc	2006-06-12 21:40:14.000000000 +0200
+++ glimmer3.02/src/Util/extract.cc	2015-05-25 22:44:01.760342470 +0200
@@ -297,7 +297,7 @@
 
   {
    fprintf (stderr,
-       "USAGE:  extract [options] <sequence-file> <coords>\n"
+       "USAGE:  glimmer_extract [options] <sequence-file> <coords>\n"
        "\n"
        "Read fasta-format <sequence-file> and extract from it the\n"
        "subsequences specified by <coords>.  By default, <coords>\n"
--- glimmer3.02.old/src/Util/Makefile	2015-05-25 22:43:12.760341653 +0200
+++ glimmer-3.02-r3/work/glimmer3.02/src/Util/Makefile	2015-05-25 23:13:34.230372010 +0200
@@ -21,7 +21,7 @@
 
 entropy-score:  entropy-score.o libGLMcommon.a
 
-extract:  extract.o libGLMcommon.a
+glimmer_extract:  extract.o libGLMcommon.a
 
 multi-extract:  multi-extract.o libGLMcommon.a