Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
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?
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 commandmuscleWin64.exe -super5 test.fasta -output alignedTest.fasta
, it gave an error.Error:
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