GitHub - mrrlab/fastcodeml: Optimization strategies for fast detection of positive selection on phylogenetic trees

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Optimization strategies for fast detection of positive selection on phylogenetic trees

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Name		Name	Last commit message	Last commit date
Latest commit History 379 Commits
extra_install_doc		extra_install_doc
simpleopt		simpleopt
.clang-format		.clang-format
.gitignore		.gitignore
AUTHORS		AUTHORS
AlignedAllocator.cpp		AlignedAllocator.cpp
AlignedAllocator.h		AlignedAllocator.h
AlignedMalloc.h		AlignedMalloc.h
BUGS		BUGS
BayesTest.cpp		BayesTest.cpp
BayesTest.h		BayesTest.h
BranchSiteModel.cpp		BranchSiteModel.cpp
BranchSiteModel.h		BranchSiteModel.h
CHANGELOG		CHANGELOG
CMakeLists.txt		CMakeLists.txt
CmdLine.cpp		CmdLine.cpp
CmdLine.h		CmdLine.h
CodeMLoptimizer.cpp		CodeMLoptimizer.cpp
CodeMLoptimizer.h		CodeMLoptimizer.h
CodonFrequencies.cpp		CodonFrequencies.cpp
CodonFrequencies.h		CodonFrequencies.h
CompilerHints.h		CompilerHints.h
DAGScheduler.cpp		DAGScheduler.cpp
DAGScheduler.h		DAGScheduler.h
Doxyfile		Doxyfile
ENSGT00390000016702.Primates.01.002.nwk		ENSGT00390000016702.Primates.01.002.nwk
ENSGT00390000016702.Primates.01.002_rooted.nwk		ENSGT00390000016702.Primates.01.002_rooted.nwk
ENSGT00390000016702.Primates.01.002_unrooted.nwk		ENSGT00390000016702.Primates.01.002_unrooted.nwk
ENSGT00390000016702.Primates.01.phy		ENSGT00390000016702.Primates.01.phy
Exceptions.h		Exceptions.h
FatVectorTransform.cpp		FatVectorTransform.cpp
FatVectorTransform.h		FatVectorTransform.h
FillMatrix.cpp		FillMatrix.cpp
Forest.cpp		Forest.cpp
Forest.h		Forest.h
ForestExport.cpp		ForestExport.cpp
ForestExport.h		ForestExport.h
ForestNode.h		ForestNode.h
Genes.cpp		Genes.cpp
Genes.h		Genes.h
HighLevelCoordinator.cpp		HighLevelCoordinator.cpp
HighLevelCoordinator.h		HighLevelCoordinator.h
INSTALL		INSTALL
LICENSE		LICENSE
MathSupport.h		MathSupport.h
MatrixSize.h		MatrixSize.h
Newick.cpp		Newick.cpp
Newick.h		Newick.h
NewickGrammar.h		NewickGrammar.h
ParseParameters.cpp		ParseParameters.cpp
ParseParameters.h		ParseParameters.h
Phylip.cpp		Phylip.cpp
Phylip.h		Phylip.h
PhyloTree.cpp		PhyloTree.cpp
PhyloTree.h		PhyloTree.h
ProbabilityMatrixSet.cpp		ProbabilityMatrixSet.cpp
ProbabilityMatrixSet.h		ProbabilityMatrixSet.h
README		README
SETPATHS		SETPATHS
THANKS		THANKS
TODO		TODO
Timer.h		Timer.h
TransitionMatrix.cpp		TransitionMatrix.cpp
TransitionMatrix.h		TransitionMatrix.h
TreeAndSetsDependencies.cpp		TreeAndSetsDependencies.cpp
TreeAndSetsDependencies.h		TreeAndSetsDependencies.h
TreeNode.cpp		TreeNode.cpp
TreeNode.h		TreeNode.h
Types.h		Types.h
VerbosityLevels.cpp		VerbosityLevels.cpp
VerbosityLevels.h		VerbosityLevels.h
WriteResults.cpp		WriteResults.cpp
WriteResults.h		WriteResults.h
blas.h		blas.h
clean.sh		clean.sh
create_tarball.sh		create_tarball.sh
fast.cpp		fast.cpp
fast.supp		fast.supp
fastcodeml.git.kdev4		fastcodeml.git.kdev4
format.sh		format.sh
genQ.r		genQ.r
lapack.h		lapack.h
nlopt.h		nlopt.h
nlopt.hpp		nlopt.hpp

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This is the FastCodeML evaluation package including sources and a precompiled executable. This package is currently for evaluation purposes only. 

Read INSTALL for installation instructions!

Usage, e.g.:

./fast -m 22 -bl -nt 1 -hy 0  ENSGT00390000016702.Primates.01.002.nwk  ENSGT00390000016702.Primates.01.phy

Above execution estimates the log likelihood for hypothesis 0 and the foreground specified in the Newick file using only one thread. The output could be like the following:

===

Doing foreground branch(es) from tree file 
-------------------------------------------
Doing foreground branch(es)  0 

LnL0: -2393.300017592994664 Function calls: 365	  

  0.2544410  0.1691760  0.1998330  0.0446050  0.0153330  0.0101750  0.0050080  0.0084390
  0.0253000  0.1309500  0.0743030

p0:  0.4858354  p1:  0.5141646  p2a:  0.0000000  p2b:  0.0000000
w0:  0.0000010  k:   5.1252258


Final Annotated Newick Tree (*N marks the branch N)

((a001:0.169176*1,a002:0.199833*2)#1:0.254441*0,(((a003:0.005008*6,a004:0.008439*7):0.010175*5,a005:0.025300*8):0.015333*4,a006:0.130950*9):0.044605*3,a007:0.074303*10):0.000000;

((a001:0.169176,a002:0.199833)#1:0.254441,(((a003:0.005008,a004:0.008439):0.010175,a005:0.025300):0.015333,a006:0.130950):0.044605,a007:0.074303):0.000000;

Time used: 0m:22s
Cores used: 1

===