--- a/csrc/dnapars.c
+++ b/csrc/dnapars.c
@@ -77,41 +77,43 @@
 /* function prototypes */
 
 
-Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
+extern Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
      weightfilename[FNMLNGTH];
 char basechar[32]="ACMGRSVTWYHKDBNO???????????????";
-node *root;
-long chars, col, msets, ith, njumble, jumb, maxtrees;
+extern node *root;
+extern long chars, col, msets, ith, njumble, jumb;
+long maxtrees;
 /*   chars = number of sites in actual sequences */
-long inseed, inseed0;
-double threshold;
-boolean jumble, usertree, thresh, weights, thorough, rearrfirst,
-          trout, progress, stepbox, ancseq, mulsets, justwts, firstset, mulf,
-          multf;
+extern long inseed, inseed0;
+extern double threshold;
+boolean thorough, rearrfirst, mulf, multf;
+extern boolean justwts, ancseq, weights, thresh, jumble, usertree, trout, mulsets, progress, stepbox, firstset;
 steptr oldweight;
-longer seed;
-pointarray treenode;            /* pointers to all nodes in tree */
-long *enterorder;
+extern longer seed;
+extern pointarray treenode;            /* pointers to all nodes in tree */
+extern long *enterorder;
 long *zeros;
 
 /* local variables for Pascal maketree, propagated globally for C version: */
 
-long minwhich;
+extern long minwhich;
 static double like, minsteps, bestyet, bestlike, bstlike2;
-boolean lastrearr, recompute;
-double nsteps[maxuser];
-long **fsteps;
-node *there, *oldnufork;
-long *place;
-bestelm *bestrees;
-long *threshwt;
+extern boolean lastrearr, recompute;
+extern double nsteps[maxuser];
+extern long **fsteps;
+extern node *there;
+node *oldnufork;
+extern long *place;
+extern bestelm *bestrees;
+extern long *threshwt;
 baseptr nothing;
-gbases *garbage;
-node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
+extern gbases *garbage;
+extern node *temp, *temp1;
+node *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
        *tmp2, *tmp3, *tmprm, *tmpadd;
-boolean *names;
+extern boolean *names;
 node *grbg;
-char *progname;
+extern char *progname;
 
 
 static void getoptions(int arg_maxtrees, dnapars_S_option s_option)
--- a/csrc/phylip.c
+++ b/csrc/phylip.c
@@ -35,6 +35,8 @@
 
 #include "phylip.h"
 
+boolean javarun;
+
 #ifdef WIN32
 #include <windows.h>
 /* for console code (clear screen, text color settings) */
--- a/csrc/phylip.h
+++ b/csrc/phylip.h
@@ -342,7 +342,7 @@
 /* Lower-triangular format. */
 #define MAT_LOWERTRI    (MAT_LOWER | MAT_MACHINE)
 
-boolean javarun;
+extern boolean javarun;
 
 typedef long *steptr;
 typedef long longer[6];
@@ -363,7 +363,6 @@
 extern boolean ibmpc, ansi, tranvsp;
 //extern naym *nayme;                     /* names of species */
 extern char* *nayme;                     /* names of species */
-boolean firstplotblock; // for debugging BMP output
 
 #define ebcdic          EBCDIC
 
--- a/csrc/protpars.c
+++ b/csrc/protpars.c
@@ -127,7 +127,7 @@
 node *temp, *temp1;
 Char ch;
 aas tmpa;
-char *progname;
+extern char *progname;
 
 /* Local variables for maketree, propagated globally for c version: */
 long minwhich;