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baoxingsong / AnchorWave

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
MIT License
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How to combine the pairwise alignments into multiple sequence alignments？ #70

Closed socialhang closed 3 months ago

socialhang commented 5 months ago

@baoxingsong Hello！

I'm pleased to have a seamless experience with your software, but I do have some queries while using it. How can I utilize pairwise alignments to achieve multiple sequence alignments? Additionally, are there any user-friendly downstream tools available for this purpose?

wjwei-handsome commented 5 months ago

Hi @socialhang !

I have some practical experience in this, and I hope this can help you.

I developed a tool to generate a pseudo-maf, which produces multi-sequence alignment of other query genomes for each reference genome.

For details and examples, you can read here : https://github.com/wjwei-handsome/wgatools?tab=readme-ov-file#experimental-generate-pseudo-maf-from-all-to-all-paf

Please let me know if you have better suggestions and other needs:)

Best wishes, Wenjie

socialhang commented 5 months ago

Thanks a lot! I will try!

Hang Zong

@. | ---- Replied Message ---- | From | @.> | | Date | 3/31/2024 14:08 | | To | @.> | | Cc | @.> , @.***> | | Subject | Re: [baoxingsong/AnchorWave] How to combine the pairwise alignments into multiple sequence alignments？ (Issue #70) |

Hi @socialhang !

I have some practical experience in this, and I hope this can help you.

I developed a tool to generate a pseudo-maf, which produces multi-sequence alignment of other query genomes for each reference genome.

For details and examples, you can read here : https://github.com/wjwei-handsome/wgatools?tab=readme-ov-file#experimental-generate-pseudo-maf-from-all-to-all-paf

Please let me know if you have better suggestions and other needs:)

Best wishes, Winnie

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

socialhang commented 5 months ago

@wjwei-handsome

I am writing to express my keen interest in trying out wgatools. However, I am encountering difficulties installing it from GitHub. I am wondering if you happen to have a compiled version for CentOS 7 or a mature Docker image available?

Your assistance in this matter would be greatly appreciated.

Thank you for your attention to this inquiry.

Best regards,

wjwei-handsome commented 5 months ago

@socialhang

This issue should not belong to this anchorwave repo.

You can open a new issue under wgatools for moving discussion.