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Do you support ClustalOmega in Biopython ? #177

Closed ASQWZXED closed 3 years ago

ASQWZXED commented 3 years ago

Hello, I haven't installed Biopython yet. I have two questions about it. 1- Does Biopython support ClustalOmega ? If yes, can I align a data that is 5.5 MB on my regular PC using it? 2- When I have already aligned MSA data, can I convert it to SNP profiles using Biopython?

Thank you.

peterjc commented 3 years ago

This repository and issue tracker are intended for our website, https://github.com/biopython/biopython is the code itself.

As to Q1, yes we have a wrapper to help invoke ClustalOmega, and support for parsing the Clustal format alignments it generates in Bio.AlignIO under the format name "clustal"

https://biopython.org/docs/dev/api/Bio.Align.Applications.html#Bio.Align.Applications.ClustalOmegaCommandline https://biopython.org/docs/dev/api/Bio.AlignIO.html https://biopython.org/wiki/AlignIO

As to Q2, I don't know what exactly you want. I suggest you ask on our mailing list https://biopython.org/wiki/Mailing_lists or the main repository, and please give more details such as a link to the desired output format, or a small example.