Question: How to use R programming for MSA and phylogenetics analysis?
gravatar for BIOAWY
5 days ago by
BIOAWY0 wrote:

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.

ADD COMMENTlink modified 4 days ago by Jean-Karim Heriche14k • written 5 days ago by BIOAWY0
gravatar for Jean-Karim Heriche
4 days ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche14k wrote:

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).

ADD COMMENTlink written 4 days ago by Jean-Karim Heriche14k
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