Issue in Muscle Alignment using Windows 8?

[Abbas Khan]

When using Bio3d in R I am facing the following problem please help me anyone. Error in seqaln(seqs) : You do not have muscle installed/working locally on your machine. We can attempt to use the EBI webserver if you provide an email address (required by the EBI). Please note that the EBI states (see their Terms of Use): 'Using fake e-mail address may result in your jobs being killed and your IP, Organisation or entire domain being black-listed.' In addition: Warning message: running command 'muscle -version' had status 127

[Lars Skjærven]

Hi Abbas, This means exactly what it says - muscle can not be found on your system. For Windows OS you'll need to specify the path to where you have installed muscle. Alternatively, use the online version of muscle:

seqaln(seq, web.args = list(email = "[e-mail]"))

Good luck. L

[Abbas Khan]

thank you but it is showing the following error again while the alignment is done already.

Warning message: running command 'muscle -version' had status 127

[Lars Skjærven]

Check the output from the seqaln() function. It's probably fine as there is no error (only a warning that it can not find muscle). Reopen issue if needed