Question: Plylogenetic tree construction
0
gravatar for majeedaasim
3.1 years ago by
majeedaasim50
United States
majeedaasim50 wrote:

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

ADD COMMENTlink modified 3.1 years ago by KVC_bioinfo510 • written 3.1 years ago by majeedaasim50
2
gravatar for Sej Modha
3.1 years ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

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

ADD COMMENTlink written 3.1 years ago by Sej Modha4.7k
0
gravatar for Cupton
3.1 years ago by
Cupton70
Victoria, BC, Canada
Cupton70 wrote:

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

ADD COMMENTlink written 3.1 years ago by Cupton70
0
gravatar for KVC_bioinfo
3.1 years ago by
KVC_bioinfo510
Boston
KVC_bioinfo510 wrote:

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 COMMENTlink written 3.1 years ago by KVC_bioinfo510
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