diff --git a/docs/doxygen.conf.in b/docs/doxygen.conf.in
index 5f041ce..66161f9 100644
--- a/docs/doxygen.conf.in
+++ b/docs/doxygen.conf.in
@@ -220,12 +220,6 @@
 
 ALIASES                =
 
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding "class=itcl::class"
-# will allow you to use the command class in the itcl::class meaning.
-
-TCL_SUBST              =
-
 # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
 # only. Doxygen will then generate output that is more tailored for C. For
 # instance, some of the names that are used will be different. The list of all
@@ -968,13 +962,6 @@
 
 ALPHABETICAL_INDEX     = YES
 
-# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
-# which the alphabetical index list will be split.
-# Minimum value: 1, maximum value: 20, default value: 5.
-# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
-
-COLS_IN_ALPHA_INDEX    = 5
-
 # In case all classes in a project start with a common prefix, all classes will
 # be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
 # can be used to specify a prefix (or a list of prefixes) that should be ignored
@@ -1989,12 +1976,6 @@
 
 EXTERNAL_PAGES         = YES
 
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of 'which perl').
-# The default file (with absolute path) is: /usr/bin/perl.
-
-PERL_PATH              = /usr/bin/perl
-
 #---------------------------------------------------------------------------
 # Configuration options related to the dot tool
 #---------------------------------------------------------------------------
@@ -2008,15 +1989,6 @@
 
 CLASS_DIAGRAMS         = YES
 
-# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see:
-# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where
-# the mscgen tool resides. If left empty the tool is assumed to be found in the
-# default search path.
-
-MSCGEN_PATH            =
-
 # If set to YES, the inheritance and collaboration graphs will hide inheritance
 # and usage relations if the target is undocumented or is not a class.
 # The default value is: YES.
@@ -2030,7 +2002,7 @@
 # set to NO
 # The default value is: NO.
 
-HAVE_DOT               = YES
+HAVE_DOT               = @HAVE_DOT@
 
 # The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
 # to run in parallel. When set to 0 doxygen will base this on the number of
@@ -2146,7 +2118,7 @@
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALL_GRAPH             = YES
+CALL_GRAPH             = NO
 
 # If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
 # dependency graph for every global function or class method.
@@ -2157,7 +2129,7 @@
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALLER_GRAPH           = YES
+CALLER_GRAPH           = NO
 
 # If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
 # hierarchy of all classes instead of a textual one.