seqaln() cannot access muscle installed through bioconductor

[Former user]

I installed MUSCLE in R through Bioconductor. Then I want to use pdbaln() that will call underlying function seqaln(). However seqaln() could not invoke MUSCLE. I know I can use muscle() directly for multiple sequence alignment. But if I want to access it through bio3d using seqaln() so that seqidentity() can use the aligned result, how should I do it?

[Xinqiu Yao]

Hi,

Make sure your installed MUSCLE is in the PATH and the command name is 'muscle'. A simple test is to type 'muscle' in a terminal and see if it shows help message. It it gives an error, you need to figure out first where the muscle is installed and what it is named. Then, provide the full path to the muscle program to seqaln() via the argument 'exefile'. For example,

aln <- seqaln(seqs, exefile='/path/to/muscle/name_of_your_muscle')

[Barry Grant]

The muscle required here is the standalone exe not a bioconductor package - see the help file for details: http://thegrantlab.org/bio3d/html/seqaln.html

These previous Q&A posts may also help: https://bitbucket.org/Grantlab/bio3d/issue/206/unable-to-launch-muscle-package-from

https://bitbucket.org/Grantlab/bio3d/issue/145/where-should-be-muscle-or-dssp-placed