Plylogenetic tree construction

Question

[majeedaasim]

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

Answer 1

[Sej Modha]

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

Answer 2

[Cupton]

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

Answer 3

[KVC_bioinfo]

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