D, H, S, B values

[Jorge Del Rosario]

Hi! 

I'm developing generax analysis and in the reconciliated.nhx file some parameters are showed. But is unclear to me how to interpret B values. What does it means and how to interpret this values?

Thanks!

[Benoit Morel]

Hello!

I am not quite sure anymore. NHX has been added for people who used to use Notung, but we rather work with the RecPhyloML format. I don't think B has a meaning in the context of reconciliation. It might be bootstrap values coming from the gene trees used as starting tree for generax. In this case you can consider them meaningless. If you want me to check, you can send me one such output nhx file.

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[Stefan Flaumberg]

Hi Jorge and Benoit,

From what is written in the source code:

For each branch of a reconciled gene tree, the NHX format provides description only for the terminal event on this gene branch (so events such as speciation-loss or transfer-loss are not shown, for they cannot be terminal) using the following fields:

:S=(species_label) -- on which species branch the event occured (the species branch name is provided)

:D=(Y/N) -- whether the event is a gene duplication (yes or no)

:H=(Y/N)(@src@dest) -- whether the event is a gene transfer (yes or no; the transfer source and destination species are provided in case of yes)

:B=(length) -- the length of the current gene branch

Thus, the overall format for a single gene branch is:

<gene_id>[&&NHX:S=<species_label>:D=<Y/N>:H=<Y/N><@src@dest>:B=0] for the gene tree root

<gene_id>:<length>[&&NHX:S=<species_label>:D=<Y/N>:H=<Y/N><@src@dest>:B=<length>] for all other gene tree nodes

So Benoit is right that :B= value has little meaning here, as the value is usually a duplicate of what follows the <gene_id> field. (Yet it is a gene branch length, not a bootstrap support).

Hope this helps!

Best,

Stefan

[Jorge Del Rosario]

Thanks for your answer. I was confused as the B values didn't correspond to any previous values.

Another question I have is related to gain and loss rates. With my calibrated species tree, I understand that a 0.283 value could be interpreted as 0.283 gain/loss genes by MY?

Thanks

Jorge 

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