[phylocom-user] FW: Phylocom Problem

Emma Jardine E.C.Jardine at student.reading.ac.uk
Fri Jul 12 02:25:44 PDT 2013


Hi all,



I am currently undertaking a project using Phylocom to look for patterns in medicinal plant use and am using the function nodesig to identify medicinally rich plant groups. I have two questions and have attached the relevant input and results files. I have been using model 0 shuffling labels across the phylogeny.



1.    I have used the function nodesigl to get a list of the numbers of taxa in the hot nodes identified by nodesig.  However the + nodes listed here do not exactly match those listed by nodesig and include some terminal taxa that are not in my sample? Am I doing something wrong?



2.    Nodesig has listed the clade with the most common recent ancestor Ischaemum - Microstegium as a hot node containing 5 medicinal genera. It has then listed an expanded clade with this one nested within as a hot node but this larger clade still only contains 5 medicinal taxa. I am a little confused as to why this would happen?



Any help greatly Appreciated



Emma Jardine
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