Merge pull request #160 from stephaneguindon/optAAFreq

Changed boundaries for GTR param values

doc/phyml-manual.tex

@@ -606,9 +606,9 @@ \subsection{Command-line interface}
 \item \x{--free\_rates} or \x{--freerates} \index{command-line options!\x{--free\_rates}}\\
 As an alternative to the discrete gamma model, it is possible to estimate the (relative) rate in
 each class of the (mixture) model and the corresponding frequencies directly from the data. This
-model, called the FreeRate model, has more parameters
+model, called FreeRate, has more parameters
 than the discrete gamma one but usually provides a significantly better fit to the data. See
-\cite{soubrier12} for more information about this model and an illustration of its use.
+\cite{soubrier12} for more information about this model and an illustration of its use. 
 
 \item \x{--il} \index{command-line options!\x{--il}}\\ \x{il} stands here for integrated (branch)
   length. This model, described in \cite{guindon13} in the context of molecular dating, provides an

src/utilities.h

@@ -171,8 +171,8 @@ static inline int isinf_ld (long double x) { return isnan (x - x); }
 #define  PINV_MIN 0.00001
 #define  PINV_MAX 0.99999
 
-#define RR_MIN 0.01
-#define RR_MAX 100.0
+#define RR_MIN 0.001
+#define RR_MAX 1000.0
 
 #define UNSCALED_RR_MIN log(RR_MIN)
 #define UNSCALED_RR_MAX log(RR_MAX)