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Methodology Questions >> How to >> branch site analysis http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1280089460 Message started by Matt on Jul 25th, 2010 at 1:24pm |
Title: branch site analysis Post by Matt on Jul 25th, 2010 at 1:24pm
Hi All,
I am trying to test if selection is enhanced in 2 species relative to the rest of the tree (about 20 other species), where each of these 2 species can have different distributions for omega. The data set consistes of sequence data from a nuclear gene, between one and 3 individuals per species representative. The alleles from these individuals do not necessarily form monophyletic groups.. i.e. there is incomplete lineage sorting/transspecies polymorphism. How can I test the hypothesis that selection is enhanced in these 2 lineages, with omega varying between them? |
Title: Re: branch site analysis Post by Matt on Jul 26th, 2010 at 4:49pm
Can you do GA branch on HYPHY, my alignment is too big for GA Branch on Datamonkey?
Matt |
Title: Re: branch site analysis Post by Sergei on Jul 26th, 2010 at 4:55pm
Hi Matt,
How many sequences do you have? You can do GA Branch in HyPhy, but you need an MPI cluster for it to finish in a reasonable amount of time. Sergei |
Title: Re: branch site analysis Post by Matt on Jul 27th, 2010 at 7:42am
Hi All,
I have one dataset with 121 sequences, and another with 78. They are short however, ~300bp each. Also, I have access to a very large cluster, i.e. thousands of compute nodes, that I usually use for Illumina work, but I suppose I could put HYPHY on there. Up until now, HYPHY has been running for me on a small 16 node cluster. I'm still not quite sure how to run GABranch on HYPHY, it isn't mentioned by name, either in the .bf files or in the menu options. Thanks |
Title: Re: branch site analysis Post by Sergei on Jul 27th, 2010 at 10:21am |
Title: Re: branch site analysis Post by Matt on Jul 28th, 2010 at 2:25pm
Hi All,
Issues with the GABranch- or more likely the MPI install.. [code]macmanes@macmanes:~/hyphy/HYPHY$ /usr/lib64/mpich/bin/mpirun -np 2 ./HYPHYMPI BASEPATH=/home/macmanes/hyphy/HYPHY /home/macmanes/hyphy/GABranchFiles/ModelSelectorBranchLocal.bf Fatal error in MPI_Comm_rank: Invalid communicator, error stack: MPI_Comm_rank(106): MPI_Comm_rank(comm=0x5b, rank=0x7fffe6724f9c) failed MPI_Comm_rank(64).: Invalid communicator macmanes@macmanes:~/hyphy/HYPHY$[/code] In fact, looking at things, I can't get HYPHYMPI to run anything.. I checked out the latest version from SVN this AM. The install seemed to go fine- no errors or anything. I am using MPICH, as I can't seem to get it to compile with OpenMPI. |
Title: Re: branch site analysis Post by Sergei on Jul 29th, 2010 at 10:56am
Hi Matt,
Haven't seen this error before -- not sure what it is about. Looks like a generic MPI error, not something HYPHY specific. Try with openMPI as well, by replacing Code (] COMPILER="g++"; COMPILERC="gcc"; [/code):
in build.sh. Sergei |
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