How to use R programming for MSA and phylogenetics analysis?

Question

[WUSCHEL]

Hi I am new to bioinformatics, if possible help me with this;

I am interested in generating a phylogenetic tree for some biological pathway proteins. For this I've extracted homologs proteins sequences for Arabidopsis proteins (30 AGIS) from below organisms and now data are in FASTA format in text doc.

Nicotiana_tabacum', 'Brassica_napus', 'Brachypodium_distachyon', 'Oryza_sativa', 'Triticum_aestivum', 'Physcomitrella_patens', 'Selaginella_moellendorffii', 'Chlamydomonas_reinhardtii', 'Homo_sapiens', 'Saccharomyces_cerevisiae'

How can I run a MSA in R program and draw a phylogenetic tree for all the interested proteins?

I am wondering if anyone can guide me with the steps.

Answer 1

[Jean-Karim Heriche]

For multiple sequence alignments, you can use the Bioconductor package msa. For phylogenetic analysis and trees, there are several R packages such as ape, phangorn, phytools (which I think combines ape with some other packages).