[med-svn] r5964 - trunk/packages/clonalframe/trunk/debian

[Andreas Tille]

Author: tille
Date: 2011-02-12 18:49:21 +0000 (Sat, 12 Feb 2011)
New Revision: 5964

Modified:
   trunk/packages/clonalframe/trunk/debian/ClonalFrame.1
Log:
Better man page


Modified: trunk/packages/clonalframe/trunk/debian/ClonalFrame.1
===================================================================
--- trunk/packages/clonalframe/trunk/debian/ClonalFrame.1	2011-02-12 18:37:37 UTC (rev 5963)
+++ trunk/packages/clonalframe/trunk/debian/ClonalFrame.1	2011-02-12 18:49:21 UTC (rev 5964)
@@ -20,9 +20,7 @@
 Sets the number of iterations between samples (default is 100)
 .TP
 \fB\-e\fR NUM
-Sets the number of branch\-swapping moves per iterations (default
-.IP
-is so that half of the time is spent branch\-swapping)
+Sets the number of branch\-swapping moves per iterations (default is so that half of the time is spent branch\-swapping)
 .TP
 \fB\-m\fR NUM
 Sets the initial value of theta to NUM (default is Watterson estimate)
@@ -61,21 +59,32 @@
 Remove all gaps at non\-polymorphic positions
 .TP
 \fB\-t\fR NUM
-Indicate which initial tree to use: 0 for a null tree, 1 for a
-.IP
-uniformly chosen coalescent tree and 2 for UPGMA tree (default)
+Indicate which initial tree to use: 0 for a null tree, 1 for a uniformly chosen coalescent tree and 2 for UPGMA tree (default)
+.TP
 \fB\-w\fR FILE     Use Newick file for initial tree
+.TP
 \fB\-a\fR NUM      Sets the first parameter of the beta prior distribution of nu
+.TP
 \fB\-b\fR NUM      Sets the second parameter of the beta prior distribution of nu
+.TP
 \fB\-U\fR          Use uniform priors for rho, theta and delta
+.TP
 \fB\-B\fR          Run in BURST mode
+.TP
 \fB\-C\fR          Run in UPGMA mode with a site\-by\-site boostrap procedure
+.TP
 \fB\-c\fR          Run in UPGMA mode with a fragment\-by\-fragment boostrap procedure
+.TP
 \fB\-S\fR NUM      Sets the seed for the random number generator to NUM
+.TP
 \fB\-E\fR NUM      Sets the rate of exponential growth (default is 0)
+.TP
 \fB\-I\fR          Ignores first block in the alignment
+.TP
 \fB\-L\fR          Clean\-up the alignment before running ClonalFrame
+.TP
 \fB\-l\fR          Minimum distance between two reference sites (default is 50)
+.TP
 \fB\-v\fR          Verbose mode
 .SH AUTHOR
 \fBClonalFrame\fP was written by Xavier Didelot.