Loading multiple sequence alignment fasta file for ggmsa

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2.1 years ago

snowpin • 0

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.

ggmsa • 1.2k views

ADD COMMENT • link 2.1 years ago by snowpin • 0

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

ADD REPLY • link 2.1 years ago by iraun 6.2k

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

ADD REPLY • link 2.1 years ago by snowpin • 0

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