constructing phylogenetic tree using phangorn

Question

[sunilthorat]

Can anybody please help me in constructing phylogenetic tree using phangorn software on R. I am new to R and Phangorn please provide me basic steps to perform the construction of phylogenetic tree.

Answer 1

[Michael]

Read the documentation: https://cran.r-project.org/web/packages/phangorn/vignettes/Trees.pdf

Hope it helps.

[sunilthorat]

Dear Michael,

Thanks for sending me the link. I would be more thankful if you could help me in providing the steps in constructing a tree from my .fasta files or .ph/*.tre files using Phangorn.

Thanks in advance

Sunil

[Michael]

You need a multiple sequence alignment as input as for almost any phylogenetics program. Search biostar for multiple sequence alignment. https://www.biostars.org/local/search/page/?q=multiple+sequence+alignment

[sunilthorat]

Dear Michael,

I have MSA file in the form of .ph and also I converted it into .nex, .tre format. Now I want to use Phangorn to build a phylogenetic tree, can you please provide commands to do so.

Thanks in advance.

Sunil