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Question: Rooted tree from MUSCLE
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gravatar for KVC_bioinfo
3.2 years ago by
KVC_bioinfo • 510
Boston
KVC_bioinfo • 510 wrote:

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.
#muscle #cwl #rootedtree • 1.2k views
ADD COMMENT • link •
modified 3.2 years ago by Jean-Karim Heriche ♦ 23k • written 3.2 years ago by KVC_bioinfo • 510
2
gravatar for Jean-Karim Heriche
3.2 years ago by
Jean-Karim Heriche ♦ 23k
EMBL Heidelberg, Germany
Jean-Karim Heriche ♦ 23k wrote:

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.
ADD COMMENT • link written 3.2 years ago by Jean-Karim Heriche ♦ 23k

Thank you very much. The book chapter you referred cleared my concept

ADD REPLY • link written 3.2 years ago by KVC_bioinfo • 510

Could you tell me the name of the book? It would be interesting to look at it.

ADD REPLY • link written 3.2 years ago by KVC_bioinfo • 510

Encyclopedia of Evolutionary Biology,

ADD REPLY • link written 3.2 years ago by Jean-Karim Heriche ♦ 23k

Thank you very much.

ADD REPLY • link written 3.2 years ago by KVC_bioinfo • 510
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