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rcedgar / muscle

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.
https://drive5.com/muscle
GNU General Public License v3.0
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-maketree is showing invalid command line #14

Closed IRSINGH27 closed 2 years ago

IRSINGH27 commented 2 years ago

muscle -maketree -in MSA_RESULT.afa -out re.phy

Invalid command line Unknown option maketree

muscle version- muscle 5.0.1428_win64

rcedgar commented 2 years ago

maketree is not a command in v5 (it is an old command in v3).

IRSINGH27 commented 2 years ago

maketree is not a command in v5 (it is an old command in v3).

so for making tree do we have some new commands or we have download v3?

rcedgar commented 2 years ago

Muscle is for making alignments, not trees -- why are you using maketree?

IRSINGH27 commented 2 years ago

Muscle is for making alignments, not trees -- why are you using maketree?

because i want to see phylogeny relationship between sequences after msa and onlive converter or mega is not able to do so thats why i was looking if muscle has some inbuilt feature for it

rcedgar commented 2 years ago

muscle (any version) is not designed to make accurate phylogenetic trees, you should use a different algorithm.