diff -up EMBOSS-6.3.1/emboss/tfm.c.debug EMBOSS-6.3.1/emboss/tfm.c
--- EMBOSS-6.3.1/emboss/tfm.c.debug	2010-04-13 10:25:56.000000000 -0400
+++ EMBOSS-6.3.1/emboss/tfm.c	2010-10-27 12:24:56.921890915 -0400
@@ -272,6 +272,12 @@ static AjBool tfm_FindAppDoc(const AjPSt
 			     AjBool html, AjPStr* path)
 {
     ajStrAssignS(path, docroot);
+    /* We're looking for a program's docs. */
+    ajStrAppendC(path, "/programs/");
+    if(html)
+	ajStrAppendC(path, "html/");
+    else
+	ajStrAppendC(path, "text/");
     ajStrAppendS(path, program);
 
     if(html)