Loading multiple sequence alignment fasta file for ggmsa
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?
- I have been loading my MSA with the following...
align <- read.alignment("my_protein_alignment.fasta",format = "fasta")
- And then use the following to create a figure...
ggmsa(align, 1, 100, color = "Clustal", font = "DroidSansMono", char_width = 0.5, seq_name = TRUE )
- However, I get this error...
Error in prepare_msa(msa) : multiple sequence alignment object no supported...
How can I fix this? Thanks in advance.
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Hi! I guess that
alignvariable contains the output ofmsa, right? Can you show the command you used for runningmsa?Yes, the
alignvariable contains my msa, which I made with mafft (mafft --auto input_sequences.fasta).