Hello dear researchers!
Well, I have a little issue about how to run a dendrogram using a binary character matrix (1 = present 0 = absent) with the software MESQUITE 3.04. I already ran a UPGMA dendrogram and its just great, but I want a little more... I'll explain:
My character matrix is about some organisms and a bunch of characteristics, but some characteristics are more important than others, so I know (in theory) you can assign different "weights" to this characters, I mean its more important Character1 than Char2, but Char2 is equally important than Char3 and more important than Char4, in numbers will be like:
Char1 = 1
Char2 = 2
Char3 = 2
Char4 = 3
And if an organism have char1 and 2, and another organism have 1 and 3, and another one have char1 and 4, the first two organisms will be together in a clade and separated will be the third one, right?
So, I can't figure out how can I do this in mezquite or R (I found some dendrogram construction using r but not something like this).
Hope someone could help me out with this little issue, I just want to know how this organisms are grouped in with weighted characters.
Thank you and take care everybody!
Alex.
https://cran.r-project.org/web/packages/WeightedCluster/vignettes/WeightedCluster.pdf
Dear Alejandro,
in Mesquite you can do it as follows:
- go to the Characters Tab (the icon with C in the bottom left or Characters > List of Characters
- on the top click on "Columns" > Current Weights and a new column will appear.
- Select the character(s) you want and click the arrow on the top of Weights column and select "Set Weights"
Hope it works, but in general check also the wiki page of Mesquite for further info.
Alternatively, if you run the analysis in TNT you can set the character weight in there as well in Data> Character Settings. You select the characters you want and you click on "of weight" to set it up.
Saludos!
https://mesquiteproject.wikispaces.com/
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