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julibinho / MobiLLe

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Newick format output #2

Closed slowsmile closed 1 year ago

slowsmile commented 1 year ago

Hi this is Xiao again, I wonder if MobiLLe could output the cluster in Newick format so that user could easily reconstruct a tree view from the clonal sequences? Thanks

julibinho commented 1 year ago

Dear Xiao,

Thanks a lot for your feedback. However, MobiLLe did not reconstruct B-cell lineage Trees, so it is not possible to provide output in newick format. Maybe you are interested in try other tools of our group: https://github.com/julibinho/ClonalTree http://www.lcqb.upmc.fr/viclod/

thanks again,

slowsmile commented 1 year ago

Thanks a lot Juliana !

Yes ClonalTree is the exact program I want. BTW, this tool appears to be only applicable to heavy chains, what if I have light chains in the input as well?

In my case, I have a set of antibody sequences (raised from the same immunogen) and I would like to generate a phylogenetic tree out of it. These sequences could include light chains as well.

Thanks a lot Best Xiao

On Tue, Mar 14, 2023 at 9:59 AM julibinho @.***> wrote:

Dear Xiao,

Thanks a lot for your feedback. However, MobiLLe did not reconstruct B-cell lineage Trees, so it is not possible to provide output in newick format. Maybe you are interested in try other tools of our group: https://github.com/julibinho/ClonalTree http://www.lcqb.upmc.fr/viclod/

thanks again,

— Reply to this email directly, view it on GitHub https://github.com/julibinho/MobiLLe/issues/2#issuecomment-1468155672, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABCXLPB3WKRT6QP5EVI7G7DW4B2S3ANCNFSM6AAAAAAVZC3Y5U . You are receiving this because you authored the thread.Message ID: @.***>

julibinho commented 1 year ago

Dear Xiao,

SOrry for this delay. In principal, you can use ClonalTree with light chain sequences. You have just to provide the naive sequence to place the root.

Best regards, Juliana

slowsmile commented 1 year ago

Thanks a lot, really appreciate your reply! Xiao

On Wed, Mar 29, 2023 at 8:41 PM julibinho @.***> wrote:

Dear Xiao,

SOrry for this delay. In principal, you can use ClonalTree with light chain sequences. You have just to provide the naive sequence to place the root.

Best regards, Juliana

— Reply to this email directly, view it on GitHub https://github.com/julibinho/MobiLLe/issues/2#issuecomment-1488530970, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABCXLPDCYPOLLR2V5MDFKSLW6QUZLANCNFSM6AAAAAAVZC3Y5U . You are receiving this because you authored the thread.Message ID: @.***>

julibinho commented 1 year ago

Done.