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. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
