Error while using super5 command

Dear developer,

From the manual https://drive5.com/muscle5/manual/cmd_super5.html, I noticed there is an option - Super5 - for aligning large sets of sequences. However, while testing with this option with the command muscleWin64.exe -super5 test.fasta -output alignedTest.fasta, it gave an error.

Error:

Invalid command line option "super5"

MUSCLE v3.8.31 by Robert C. Edgar

http://www.drive5.com/muscle
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

Basic usage

    muscle -in <inputfile> -out <outputfile>

Common options (for a complete list please see the User Guide):

    -in <inputfile>    Input file in FASTA format (default stdin)
    -out <outputfile>  Output alignment in FASTA format (default stdout)
    -diags             Find diagonals (faster for similar sequences)
    -maxiters <n>      Maximum number of iterations (integer, default 16)
    -maxhours <h>      Maximum time to iterate in hours (default no limit)
    -html              Write output in HTML format (default FASTA)
    -msf               Write output in GCG MSF format (default FASTA)
    -clw               Write output in CLUSTALW format (default FASTA)
    -clwstrict         As -clw, with 'CLUSTAL W (1.81)' header
    -log[a] <logfile>  Log to file (append if -loga, overwrite if -log)
    -quiet             Do not write progress messages to stderr
    -version           Display version information and exit

Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2
Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3
Fastest possible (nucleotides): -maxiters 1 -diags

I have tested run with the normal run with this command: `muscleWin64.exe -in test.fasta -out alignedTest.fasta. The tool is run properly. So, do you have any suggestions to solve this problem?

Best regards, Li Chuin Chong

rcedgar / muscle

Error while using super5 command #33