Loading multiple sequence alignment fasta file for ggmsa

Question

[snowpin]

Hello,

I am trying to use ggmsa to visualize my amino acid multiple sequence alignment (MSA) but the ggmsa() function doesn't recognize my MSA. Any thoughts how I can correct this?

1. I have been loading my MSA with the following...

align <- read.alignment("my_protein_alignment.fasta",format = "fasta")

1. And then use the following to create a figure...

ggmsa(align, 1, 100, color = "Clustal", font = "DroidSansMono", char_width = 0.5, seq_name = TRUE )

1. However, I get this error...

Error in prepare_msa(msa) : multiple sequence alignment object no supported...

How can I fix this? Thanks in advance.

[iraun]

Hi! I guess that align variable contains the output of msa, right? Can you show the command you used for running msa ?

[snowpin]

Yes, the align variable contains my msa, which I made with mafft (mafft --auto input_sequences.fasta).