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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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gap penlty #61

Closed naama68 closed 1 year ago

naama68 commented 1 year ago

Hi How can I add a high gap penlty? (these are only part of MSA I a list of sequences) I would like the alignment not to start with a gap. Thanks

align

rcedgar commented 1 year ago

well, you can set all the HMM parameters, but this sounds like a very bad idea. from the examples you posted, it's clear that the N-terminals of these sequences don't align, there should be a terminal gap. if you disallow terminal gaps, you'll get one or a few letters followed by a long gap and then the block that aligns.

On Fri, Jun 16, 2023 at 7:43 AM naama68 @.***> wrote:

Hi How can I add a high gap penlty? (these are only part of MSA I a list of sequences) I would like the alignment not to start with a gap. Thanks

[image: align] https://user-images.githubusercontent.com/135230583/246449304-9cbb8bd6-02c3-4ca7-9c85-6fcc6314b014.jpg

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naama68 commented 1 year ago

thanks for the reply. I actually had a problem with the pdbs that were input. regards On 17 Jun 2023, at 2:21, Robert Edgar @.***> wrote: well, you can set all the HMM parameters, but this sounds like a very bad

idea. from the examples you posted, it's clear that the N-terminals of

these sequences don't align, there should be a terminal gap. if you

disallow terminal gaps, you'll get one or a few letters followed by a long

gap and then the block that aligns.

On Fri, Jun 16, 2023 at 7:43 AM naama68 @.***> wrote:

Hi

How can I add a high gap penlty?

(these are only part of MSA I a list of sequences)

I would like the alignment not to start with a gap.

Thanks

[image: align]

https://user-images.githubusercontent.com/135230583/246449304-9cbb8bd6-02c3-4ca7-9c85-6fcc6314b014.jpg

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