Question

Plylogenetic tree construction

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6.5 years ago

majeedaasim ▴ 60

I have amino acid sequences of about 900 genes from 20 species and I want to construct a phylogenetic tree from it. I read that these are to aligned first by MUSCLE and then to create a tree. I want to know what would be best tool for the construction of such a big tree.

Thanks

Sequence alignment MUSCLE Tree • 1.7k views

ADD COMMENT • link updated 6.5 years ago by KVC_bioinfo ▴ 590 • written 6.5 years ago by majeedaasim ▴ 60

score 2 · Answer 1 · 2017-11-02

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6.5 years ago

Sej Modha 5.3k

RAxML - https://sco.h-its.org/exelixis/web/software/raxml/index.html

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score 0 · Answer 2 · 2017-11-02

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6.5 years ago

Cupton ▴ 80

Be sure to view and your alignment so you can see errors.

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score 0 · Answer 3 · 2017-11-02

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6.5 years ago

KVC_bioinfo ▴ 590

You can use MUSCLE alignment for a maximum of 500 sequences or a maximum file size of 1 MB. The choice of tool for phylogenetic tree construction also depends on kind of tree exactly you want to look at from it.

Following two works good:

MEGA

TreeView

ADD COMMENT • link 6.5 years ago by KVC_bioinfo ▴ 590