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nselem / corason

Bioinformatic Tools for study Evolution of metabolic diversity
GNU Affero General Public License v3.0
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The meaning of value substitions/site in legend #12

Closed huizhen2014 closed 9 months ago

huizhen2014 commented 9 months ago

Hello, I have successfully installed the corason and it looks working well. I found a value in the legend, substituions/site, and I checked all the tutorial and article but can't find the introduction about it. Could you give a a explanation? Thanks a lot. This software is awesome.

nselem commented 9 months ago

Hello, Thanks for using CORASON. I'm not sure which value you mention; could you give an example?

huizhen2014 commented 9 months ago

Thanks, I post a capture on your tutorial website, and using red arrow and frame to highlight it: 1

nselem commented 9 months ago

Oh, I see. That legend comes from fasttree. CORASON first found the core genes, aligned them with muscle, kept conserved sites with Gblocks, and finally ran Fasttree over these sites.

huizhen2014 commented 9 months ago

Thanks, and the core genes are searched based on the genes from reference genome? 😁

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From: Nelly Sélem @.> Sent: Tuesday, February 27, 2024 6:03:19 PM To: nselem/corason @.> Cc: HUI Zhen @.>; Author @.> Subject: Re: [nselem/corason] The meaning of value substitions/site in legend (Issue #12)

Oh, I see. That legend comes from fasttreehttp://www.microbesonline.org/fasttree/. CORASON first found the core genes, aligned them with muscle, kept conserved sites with Gblocks, and finally ran Fasttree over these sites.

— Reply to this email directly, view it on GitHubhttps://github.com/nselem/corason/issues/12#issuecomment-1966193092, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AF2K5CRYKYZN23VVCS3EMHTYVWVOPAVCNFSM6AAAAABDZ6WHTCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRWGE4TGMBZGI. You are receiving this because you authored the thread.Message ID: @.***>

nselem commented 9 months ago

The core genes are searched based on the reference BGC . Its not a full genome but a cluster of genes. Im fact the query gene in fasta is required to assure the core Will not be empty, and World contain at least the query gene and perhaps something else

huizhen2014 commented 9 months ago

Thanks a lot!😀

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From: Nelly Sélem @.> Sent: Tuesday, February 27, 2024 8:34:04 PM To: nselem/corason @.> Cc: HUI Zhen @.>; Author @.> Subject: Re: [nselem/corason] The meaning of value substitions/site in legend (Issue #12)

The core genes are searched based on the reference BGC . Its not a full genome but a cluster of genes. Im fact the query gene in fasta is required to assure the core Will not be empty, and World contain at least the query gene and perhaps something else

— Reply to this email directly, view it on GitHubhttps://github.com/nselem/corason/issues/12#issuecomment-1966447328, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AF2K5CTJ6D667IAXTVU2U73YVXHDZAVCNFSM6AAAAABDZ6WHTCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRWGQ2DOMZSHA. You are receiving this because you authored the thread.Message ID: @.***>