mapnh, count.max
42 views
Skip to first unread message
Tristan Lefebure
Jul 10, 2012, 12:07:07 PM7/10/12
to testnh-h...@googlegroups.com
Hello,
A simple question about the meaning of the count.max option of mapnh. In the MantellidFrog example it is set to 3. If not set, the default is -1. Is this the maximun number of count on a branch? (eg. 3 synonymous subst)
Thanks!
--
Tristan
A simple question about the meaning of the count.max option of mapnh. In the MantellidFrog example it is set to 3. If not set, the default is -1. Is this the maximun number of count on a branch? (eg. 3 synonymous subst)
Thanks!
--
Tristan
Julien Yann Dutheil
Jul 10, 2012, 2:03:36 PM7/10/12
to testnh-h...@googlegroups.com
Hi Tristan,
It is the maximum number of counts on a branch-site, to control for
saturation. It is usually a good idea to set it, although in many data
sets it is hopefully useless !
You can get an idea of the saturation in your data by looking at the
output of mapnh, it will say how many sites are discarded for each
node. Such saturated sites will not be used in the counting and
therefore, neither in the clustering.
Hope this helps,
Julien.
--
Julien Y. Dutheil, Ph-D
0 (+49) 6421 178 530
§ Max Planck Institute for Terrestrial Microbiology
Department of Organismic Interactions
Marburg -- GERMANY
§ Intitute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE
It is the maximum number of counts on a branch-site, to control for
saturation. It is usually a good idea to set it, although in many data
sets it is hopefully useless !
You can get an idea of the saturation in your data by looking at the
output of mapnh, it will say how many sites are discarded for each
node. Such saturated sites will not be used in the counting and
therefore, neither in the clustering.
Hope this helps,
Julien.
Julien Y. Dutheil, Ph-D
0 (+49) 6421 178 530
§ Max Planck Institute for Terrestrial Microbiology
Department of Organismic Interactions
Marburg -- GERMANY
§ Intitute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE
Reply all
Reply to author
Forward
0 new messages