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ssolo / ALE

Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.
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tau flag not working? #40

Closed HGord2022 closed 1 year ago

HGord2022 commented 1 year ago

Hi there,

I'm hoping to use this great package to improve my gene tree, so I'm running ALEml_undated and using the tau=0 flag, however my .uml_rec file outputs this:

"# of Duplications Transfers Losses Speciations" Total 19 396 386 39

Which shows the number of transfers as 396, which should not be possible if I am understanding this correctly. Any clarity on this would be really useful. the command I'm using is as follows:

$ ALEml_undated species.tree final.ufboot.ale tau=0

All the best, Harry

ssolo commented 1 year ago

Could you provide the input files?On 2023. Apr 17., at 20:38, HGord2022 @.***> wrote: Hi there, I'm hoping to use this great package to improve my gene tree, so I'm running ALEml_undated and using the tau=0 flag, however my .uml_rec file outputs this: of Duplications Transfers Losses Speciations Total 19 396 386 39 Which shows the number of transfers as 396, which should not be possible if I am understanding this correctly. Any clarity on this would be really useful. the command I'm using is as follows: $ ALEml_undated species.tree final.ufboot.ale tau=0 All the best, Harry

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HGord2022 commented 1 year ago

Hi there,

Thanks so much for looking into this, I think I have just fixed the issue by using a completely bifurcating species tree to reconcile, my initial one had some multifurcations. I can still attach my initial input files if it would be helpful.

Thanks again, Harry

ssolo commented 1 year ago

Fixed, please verify.