Hello,
I have a .clw file from the MUSCLE multiple sequence alignment. I want to draw a rooted tree from it. The tree which MUSCLE provided is not rooted one.
Can any one help me?
Thank you in advance
Hello,
I have a .clw file from the MUSCLE multiple sequence alignment. I want to draw a rooted tree from it. The tree which MUSCLE provided is not rooted one.
Can any one help me?
Thank you in advance
I am assuming you have built a tree using the -maketree and neighbor-joining options of MUSCLE. There are two commonly used easy ways of rooting a tree: one is to define an outgroup, the other is called midpoint rooting and places the root in the middle of the segment between the two most distant leaves. For more details on rooting trees, see this book chapter. As for doing it in practice, you can use the root() function from the R package ape.
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Thank you very much. The book chapter you referred cleared my concept
Could you tell me the name of the book? It would be interesting to look at it.
Encyclopedia of Evolutionary Biology,
Thank you very much.