diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..20157a7
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,74 @@
+# -*- makefile -*-
+# just make headings for each thing and put the headings
+# on the line for ALL
+PROJECTDIR = .
+BINDIR = $(PROJECTDIR)
+
+CC = gcc
+CPPC = g++
+CFLAGS = -O3 -g -Wall
+LDFLAGS = -lm
+
+DEPEND_FILES = *.cc *.c *.h
+CLEANABLE_FILES = *.o *~
+
+ALL = adjust anomaly build-icm check codon-usage compare-lists \
+       extract generate get-len get-putative glimmer2 long-orfs
+
+.SUFFIXES: .cc .c
+
+.c.o:
+	$(CC) $(CFLAGS) -c $*.c -o $*.o 
+
+.cc.o:
+	$(CPPC) $(CFLAGS) -c $*.cc -o $*.o 
+
+all:    $(ALL)
+
+adjust:	adjust.o delcher.o
+	$(CPPC) -o $(BINDIR)/$@ adjust.o delcher.o $(LDFLAGS)
+
+anomaly:	anomaly.o delcher.o gene.o
+	$(CPPC) -o $(BINDIR)/$@ anomaly.o delcher.o gene.o $(LDFLAGS)
+
+build-icm:	build-icm.o misc.o
+	$(CC) -o $(BINDIR)/$@ build-icm.o misc.o $(LDFLAGS)
+
+check:	check.o delcher.o
+	$(CPPC) -o $(BINDIR)/$@ check.o delcher.o $(LDFLAGS)
+
+codon-usage:	codon-usage.o delcher.o gene.o
+	$(CPPC) -o $(BINDIR)/$@ codon-usage.o delcher.o gene.o $(LDFLAGS)
+
+compare-lists:	compare-lists.o delcher.o
+	$(CPPC) -o $(BINDIR)/$@ compare-lists.o delcher.o $(LDFLAGS)
+
+extract:	extract.o delcher.o
+	$(CPPC) -o $(BINDIR)/$@ extract.o delcher.o $(LDFLAGS)
+
+generate:	generate.o delcher.o gene.o
+	$(CPPC) -o $(BINDIR)/$@ generate.o delcher.o gene.o $(LDFLAGS)
+
+get-len:	get-len.o delcher.o
+	$(CPPC) -o $(BINDIR)/$@ get-len.o delcher.o $(LDFLAGS)
+
+get-putative:	get-putative.o delcher.o
+	$(CPPC) -o $(BINDIR)/$@ get-putative.o delcher.o $(LDFLAGS)
+
+glimmer2:	glimmer2.o delcher.o gene.o rnabin.o
+	$(CPPC) -o $(BINDIR)/$@ glimmer2.o delcher.o gene.o rnabin.o $(LDFLAGS)
+
+long-orfs:	long-orfs.o delcher.o gene.o
+	$(CPPC) -o $(BINDIR)/$@ long-orfs.o delcher.o gene.o $(LDFLAGS)
+
+rnabin:	rnabin.o delcher.o
+	$(CPPC) -o $(BINDIR)/$@ rnabin.o delcher.o $(LDFLAGS)
+
+depend:
+	makedepend $(DEPEND_FILES)
+
+clean:
+	/bin/rm -f $(CLEANABLE_FILES)
+
+# DO NOT DELETE THIS LINE -- make depend depends on it.
+
diff --git a/delcher.h b/delcher.h
new file mode 100644
index 0000000..085f135
--- /dev/null
+++ b/delcher.h
@@ -0,0 +1,120 @@
+//  A. L. Delcher
+//
+//  File:  ANNOTATION/Glimmer/delcher.h
+//  Version:  2.03  3 Dec 2002
+//
+//  Copyright (c) 2002 by Arthur Delcher, Steven Salzberg, Simon
+//  Kasif, and Owen White.  All rights reserved.  Redistribution
+//  is not permitted without the express written permission of
+//  the authors.
+//
+//  Common generic routines.
+//
+
+
+#ifndef  __DELCHER_H_INCLUDED
+#define  __DELCHER_H_INCLUDED
+
+
+#include  <stdio.h>
+#include  <stdlib.h>
+#include  <iostream.h>
+#include  <iomanip.h>
+#include  <fstream.h>
+#include  <math.h>
+#include  <string.h>
+#include  <ctype.h>
+#include  <limits.h>
+#include  <float.h>
+#include  <time.h>
+#include  <assert.h>
+#include  <errno.h>
+#include  <unistd.h>
+
+
+#define  TRUE  1
+#define  FALSE  0
+#ifndef  EXIT_FAILURE
+  #define  EXIT_FAILURE  -1
+#endif
+#ifndef  EXIT_SUCCESS
+  #define  EXIT_SUCCESS  0
+#endif
+
+
+const int  FASTA_WIDTH = 60;
+  // Max number of characters to print on a FASTA data line
+
+
+const char *  Commatize
+    (long int  n);
+void  Fasta_Print
+    (FILE * fp, char * s, char * hdr);
+void  Fasta_Print_N
+    (FILE * fp, char * s, int n, char * hdr);
+FILE *  File_Open
+    (const char *, const char *);
+double  Percent
+    (double a, double b);
+void *  Safe_calloc
+    (size_t N, size_t Len, size_t line_num = 0);
+void *  Safe_malloc
+    (size_t Len, size_t line_num = 0);
+void *  Safe_realloc
+    (void * Q, size_t Len, size_t line_num = 0);
+
+
+template <class DT>
+  DT  Max  (DT, DT);
+template <class DT>
+  DT  Min  (DT, DT);
+template <class DT>
+  void  Swap  (DT &, DT &);
+
+
+template <class DT>
+DT  Max  (DT A, DT B)
+
+//  Return the larger of  A  and  B .
+
+  {
+   if  (A > B)
+       return  A;
+     else
+       return  B;
+  }
+
+
+
+template <class DT>
+DT  Min  (DT A, DT B)
+
+//  Return the smaller of  A  and  B .
+
+  {
+   if  (A < B)
+       return  A;
+     else
+       return  B;
+  }
+
+
+
+template <class DT>
+void  Swap  (DT & A, DT & B)
+
+//  Swap the values in  A  and  B .
+
+  {
+   DT  Save;
+
+   Save = A;
+   A = B;
+   B = Save;
+
+   return;
+  }
+
+
+
+#endif
diff --git a/run-glimmer2 b/run-glimmer2
new file mode 100755
index 0000000..263bff2
--- /dev/null
+++ b/run-glimmer2
@@ -0,0 +1,16 @@
+echo "run Glimmer2"
+clear
+echo "Genome is " $1
+echo "Find non-overlapping orfs in  tmp.coord"
+rm -f tmp.coord
+long-orfs $1 | get-putative >tmp.coord
+echo "Extract training sequences to  tmp.train"
+rm -f tmp.train
+extract $1 tmp.coord >tmp.train
+wc tmp.train
+echo "Build interpolated context model in  tmp.model"
+rm -f tmp.model
+build-icm <tmp.train >tmp.model
+echo "Predict genes with Glimmer2 with coordinates in  g2.coord"
+rm -f g2.coord
+glimmer2 $1 tmp.model | get-putative >g2.coord