constraint tree

[yong...@gmail.com]

hello, everybody:
now, I am analysing DNA barcoding data, I want bulid a constraint tree to constrain my phylogenetic tree. But I do not know how to choose clades(for example, by order or by family), I have built a constraint tree by the species name,  this tree ensure every species is in its place, so I got a higher revolution in the species and genus level. I do not know if I am right? Could you help me to answer this question?
Best wishes!
XUYONG

[Alexandros Stamatakis]

your question is more biological, so I am not the right person to answer
this, but let me make a more methodological observation:

by using a constraint tree you bias the phylogenetic search a priori ...
my suggestion would be that you also run an unconstrained search and do
a likelihood significance test between the constrained and unconstrained
tree, to see to which extent imposing your prior beliefs about what the
tree should look like deteriorates the ML score ... also when doing
constrained searches, errors such as mislabeled sequences might go
undetected ... so please be careful when using constraints

alexis

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[yong...@gmail.com]

Thank you very much,Alexis. I just see it, I am very sorry. Now, I have learned  some knowledges about the constraint tree, so I knew what I will do with it.

Thank you a lot.

Best wishes.

在 2017年6月30日星期五 UTC+8下午2:53:17，Alexis写道：