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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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fractionMissing.h is missing #8

Closed maxemil closed 7 years ago

maxemil commented 7 years ago

Hej @Boussau, I just saw that you pushed an update to include fraction of missing genes in incomplete genomes! That's great! However, i guess its still a work in progress, as i am unable to build ALE with docker, getting the folowing error:

-- Configuring done
CMake Error at src/CMakeLists.txt:14 (add_library):
  Cannot find source file:

    fractionMissing.h

  Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp
  .hxx .in .txx

-- Build files have been written to: /usr/local/ALE/build

also, i needed to change the first RUN command in the Dockerfile to 

RUN apt-get update && apt-get clean

as i was getting

Step 3 : RUN apt-get clean && apt-get update
 ---> Running in b640adeb8f08
E: Could not open lock file /var/cache/apt/archives/lock - open (2: No such file or directory)
E: Unable to lock the download directory
The command '/bin/sh -c apt-get clean && apt-get update' returned a non-zero code: 100

excited to try out the version that deals with incomplete genomes!

Boussau commented 7 years ago

Hi Max Emil,

Sorry about the mess, I just pushed the two files. Regarding the docker, I'll look into it tomorrow. Thanks for your messages and sorry again!

Bastien

maxemil commented 7 years ago

Hi Bastien, Thanks for the quick reply! It compiles well now! I will start testing with some of our data now, but i am wondering what would be the syntax of the fractionMissing.txt file? Something like this for all leaves present?:

genome1<tab>0.1
genome2<tab>0.05
...

And then I would invoke with ALEml_undated $species_tree $ale_object fraction_missing="fractionMissing.txt"?

thanks again for the work!

Boussau commented 7 years ago

Hi Max Emil,

It would be: genome1:0.1 genome2:0.05 ... but I have yet to test it! So far all I checked was that the results were still the same as before when the fraction of missing genes was not provided, I have not yet checked what happens when they are provided...

maxemil commented 7 years ago

Hi Bastien, great! It runs fine so far with a sample file that i created, but i still have to see how the real data behaves and what changes in comparison to the previous version.

/max emil