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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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ALEml doesnot generate consensus tree #34

Closed meiranmeiran closed 10 months ago

meiranmeiran commented 2 years ago

Hi folks,

I compiled ALE from source on Ubuntu. Everything runs well except that ALEml_undated does not generate a consensus tree of the reconciled gene tree. When I run the same command and the same data on docker, a consensus tree is generated. I am wondering what is the cause?

Thanks, Ran

command: '/home/apps/ALE/build/bin/ALEml_undated' species_tree.newick geneFamily.treelist.ale sample=1000

stdout: ALEml_undated using ALE v1.0 Read species tree from: species_tree.newick..

0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----|

Results in: species_tree.newick_geneFamily.treelist.ale.uml_rec Transfers in: species_tree.newick_geneFamily.treelist.ale.uTs

ssolo commented 2 years ago

We had issues with the bio++ library used for consensus tree generation and disabled this feature.

Gergely

On 2022. Jul 4., at 10:28, meiranmeiran @.***> wrote:

 Hi folks,

I compiled ALE from source on Ubuntu. Everything runs well except that ALEml_undated does not generate a consensus tree of the reconciled gene tree. When I run the same command and the same data on docker, a consensus tree is generated. I am wondering what is the cause?

Thanks, Ran

command: '/home/apps/ALE/build/bin/ALEml_undated' species_tree.newick geneFamily.treelist.ale sample=1000

stdout: ALEml_undated using ALE v1.0 Read species tree from: species_tree.newick..

86 nodes loaded. Read summary of tree sample for 4000 trees from: geneFamily.treelist.ale.. \ 367 nodes loaded. Reconciliation model initialised, starting DTL rate optimisation..

optimizing delta rate

optimizing tau rate

optimizing lambda rate

optimizing rates

Optimizing... - 76 ML rates: delta=1.12315e-08; tau=0.13238; lambda=0.349294. LL=-171.526 Sampling reconciled gene trees.. 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----|

Results in: species_tree.newick_geneFamily.treelist.ale.uml_rec Transfers in: species_tree.newick_geneFamily.treelist.ale.uTs

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meiranmeiran commented 2 years ago

Gergely,

Thanks for your quick reply. Does that mean the consensus tree generated by ALE at docker have some issue too?

Ran

ssolo commented 2 years ago

No, the issue was a hard to resolve / predict segmentation fault, when you get a tree it should be fine.

On 2022. Jul 4., at 10:56, meiranmeiran @.***> wrote:

 Gergely,

Thanks for your quick reply. Does that mean the consensus tree generated by ALE at docker have some issue too?

Ran

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