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qunfengdong / BLCA

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Clustal alignment tool instead of muscle #8

Closed koopkaup closed 5 years ago

koopkaup commented 6 years ago

Because of the limitation in muscle alignment only showing maximum of 32 characters in the query ID whereas clustal (omega) doesn't have that limitation and the aligning speed is the same so I suggest switching from muscle to clustal.

I modified the python code and used clustal omega and it seems to be working. My fasta headers are longer than 32 characters and I don't want to rename them to retain compatibility with other methods.

qunfengdong commented 6 years ago

Hi. Thanks for your suggestions. Yes, we are aware of the ID length restrictions with Muscle and I am glad that you have taken steps to try it with clustal instead. Do you mind sending us your modified code? We'd like to test it and consider your suggestions in the next release. Thanks, Qunfeng

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On Mar 7, 2018, at 2:33 AM, Kristjan notifications@github.com wrote:

Because of the limitation in muscle alignment only showing maximum of 32 characters in the query ID whereas clustal (omega) doesn't have that limitation and the aligning speed is the same so I suggest switching from muscle to clustal.

I modified the python code and used clustal omega and it seems to be working. My fasta headers are longer than 32 characters and I don't want to rename them to retain compatibility with other methods.

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qunfengdong commented 6 years ago

I am away for a conference this week. If you'd like to share your code, please send it to qunfengd@gmail.com.

Sent from my iPhone

On Mar 7, 2018, at 2:33 AM, Kristjan notifications@github.com wrote:

Because of the limitation in muscle alignment only showing maximum of 32 characters in the query ID whereas clustal (omega) doesn't have that limitation and the aligning speed is the same so I suggest switching from muscle to clustal.

I modified the python code and used clustal omega and it seems to be working. My fasta headers are longer than 32 characters and I don't want to rename them to retain compatibility with other methods.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.