Commit b3676234 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.6.1+dfsg

parent 73a82c85

CMakeLists.txt

+67 −111
Original line number Diff line number Diff line
@@ -14,9 +14,9 @@ 
# Linux example usages:

#----------------------

# cmake <source_dir>						   (sequential version)

# cmake -DIQTREE_FLAGS="omp" <source_dir>      (OpenMP version)

# cmake -DIQTREE_FLAGS="m32" <source_dir>      (32-bit sequential version)

# cmake -DIQTREE_FLAGS="m32 omp" <source_dir>  (32-bit OpenMP version)

# cmake <source_dir>      (OpenMP version)

# cmake -DIQTREE_FLAGS="m32-single" <source_dir>      (32-bit sequential version)

# cmake -DIQTREE_FLAGS="m32" <source_dir>  (32-bit OpenMP version)

#

# To compile with CLANG on Linux:

# export CC=/usr/bin/clang
@@ -26,18 +26,19 @@ 
#

# Mac OSX example usages:

#------------------------

# cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ <source_dir>							(sequential version)

#

# To build OpenMP version one needs to download Clang version 3.7 or later (as of November 2015)

# Then assuming clang3.7 and clang++3.7 are the newly built compilers, then:

# cmake -DCMAKE_C_COMPILER=clang3.7 -DCMAKE_CXX_COMPILER=clang++3.7 -DIQTREE_FLAGS="omp" <source_dir>		(OpenMP version)

# cmake -DCMAKE_C_COMPILER=clang3.7 -DCMAKE_CXX_COMPILER=clang++3.7 <source_dir>   (OpenMP version)

#

# cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DIQTREE_FLAGS=single <source_dir>   (sequential version)

#





# Compile OpenMP version: cmake -DIQTREE_FLAGS=omp ....

# Compile OpenMP version: cmake ....

# Compile 32-bit version: cmake -DIQTREE_FLAGS=m32 ....

# Compile static version: cmake -DIQTREE_FLAGS=static ....

# Compile static OpenMP version: cmake -DIQTREE_FLAGS="omp static" ....

# Compile static OpenMP version: cmake -DIQTREE_FLAGS="static" ....



#NOTE: Static linking with clang windows: make a symlink libgcc_eh.a to libgcc.a (administrator required)

# C:\TDM-GCC-64\lib\gcc\x86_64-w64-mingw32\5.1.0>mklink libgcc_eh.a libgcc.a
@@ -49,8 +50,8 @@ project(iqtree) 
add_definitions(-DIQ_TREE)

# The version number.

set (iqtree_VERSION_MAJOR 1)

set (iqtree_VERSION_MINOR 5)

set (iqtree_VERSION_PATCH "5")

set (iqtree_VERSION_MINOR 6)

set (iqtree_VERSION_PATCH "1")



set(BUILD_SHARED_LIBS OFF)
@@ -153,7 +154,8 @@ elseif (CMAKE_CXX_COMPILER_ID MATCHES "Clang") 
    endif()



    # use libc++ per default in MacOS

    if (APPLE AND CMAKE_BUILD_TYPE MATCHES "Release")

    if (APPLE)

        SET(CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LIBRARY "libc++")

        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")

    endif()
@@ -252,9 +254,9 @@ endif() 
# configure OpenMP/PThreads compilation

# change the executable name if compiled for OpenMP parallel version

##################################################################

if (IQTREE_FLAGS MATCHES "omp")

if (NOT IQTREE_FLAGS MATCHES "single")

	message("OpenMP        : Yes")

	SET(EXE_SUFFIX "${EXE_SUFFIX}-omp")

	#SET(EXE_SUFFIX "${EXE_SUFFIX}-omp")

	add_definitions(-D_USE_PTHREADS)

	if (MSVC)

		add_definitions(/MT)
@@ -366,8 +368,9 @@ elseif (IQTREE_FLAGS MATCHES "avx") # AVX instruction set 
	set(COMBINED_FLAGS "${COMBINED_FLAGS} ${AVX_FLAGS}")

	#SET(EXE_SUFFIX "${EXE_SUFFIX}-avx")

elseif (NOT IQTREE_FLAGS MATCHES "nosse") #SSE intruction set

    if (IQTREE_FLAGS MATCHES "512")

    if (IQTREE_FLAGS MATCHES "KNL")

        message("Vectorization : SSE3/AVX/AVX2/AVX-512")

        add_definitions(-D__AVX512KNL)

    else()

        message("Vectorization : SSE3/AVX/AVX2")

    endif()
@@ -449,103 +452,69 @@ include_directories("${PROJECT_BINARY_DIR}") 
#include_directories("${PROJECT_BINARY_DIR}/zlib-1.2.7")





if (NOT IQTREE_FLAGS MATCHES "nozlib")

    find_package(ZLIB)

endif()



if(ZLIB_FOUND)

  message ("Using system zlib")

  include_directories(${ZLIB_INCLUDE_DIRS})

else(ZLIB_FOUND)

  message ("Using own zlib-1.2.7")

  include_directories("${PROJECT_BINARY_DIR}/zlib-1.2.7" "${PROJECT_SOURCE_DIR}/zlib-1.2.7")

  add_subdirectory(zlib-1.2.7)

endif(ZLIB_FOUND)



##################################################################

# subdirectories containing necessary libraries for the build

##################################################################

add_subdirectory(pll)

add_subdirectory(ncl)

add_subdirectory(nclextra)

add_subdirectory(utils)

add_subdirectory(pda)

add_subdirectory(lbfgsb)

add_subdirectory(whtest)

add_subdirectory(sprng)

#add_subdirectory(zlib-1.2.7)

add_subdirectory(vectorclass)

LIST(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}")

if (NOT EIGEN3_INCLUDE_DIR)

    find_package(Eigen3)

if(EIGEN3_FOUND)

  include_directories(${EIGEN3_INCLUDE_DIR})

endif(EIGEN3_FOUND)

    if(NOT EIGEN3_FOUND)

        message(FATAL_ERROR "Eigen3 library not found. Either install it or rerun cmake with -DEIGEN3_INCLUDE_DIR=<installed_eigen3_dir>")

    endif()

endif()

add_definitions("-I${EIGEN3_INCLUDE_DIR} -DUSE_EIGEN3")

add_subdirectory(model)

add_subdirectory(gsl)

add_subdirectory(alignment)

add_subdirectory(tree)



##################################################################

# the main executable

##################################################################



add_library(kernelsse phylokernelsse.cpp)

add_library(kernelsse tree/phylokernelsse.cpp)



if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")

add_library(kernelavx phylotreeavx.cpp)

add_library(kernelfma phylokernelfma.cpp)

if (IQTREE_FLAGS MATCHES "512")

    add_library(kernelavx512 phylokernelavx512.cpp)

    add_definitions(-DINCLUDE_AVX512)

add_library(kernelavx tree/phylotreeavx.cpp)

add_library(kernelfma tree/phylokernelfma.cpp)

    if (IQTREE_FLAGS MATCHES "KNL")

        add_library(kernelavx512 tree/phylokernelavx512.cpp)

    endif()

endif()



if (IQTREE_FLAGS MATCHES "mpi")

	add_library(mympi TreeCollection.cpp ObjectStream.cpp)

	add_library(mympi utils/TreeCollection.cpp utils/ObjectStream.cpp)

endif()



add_executable(iqtree

alignment.cpp alignment.h

alignmentpairwise.cpp alignmentpairwise.h

circularnetwork.cpp circularnetwork.h

eigendecomposition.cpp eigendecomposition.h

greedy.cpp greedy.h

gss.cpp gss.h

gurobiwrapper.cpp gurobiwrapper.h

gzstream.cpp gzstream.h

hashsplitset.cpp hashsplitset.h

iqtree.cpp iqtree.h

maalignment.cpp maalignment.h

matree.cpp matree.h

mexttree.cpp mexttree.h

mpdablock.cpp mpdablock.h

msetsblock.cpp msetsblock.h

msplitsblock.cpp msplitsblock.h

modelsblock.cpp modelsblock.h

mtree.cpp mtree.h

mtreeset.cpp mtreeset.h

ncbitree.cpp ncbitree.h

ngs.cpp ngs.h

node.cpp node.h

optimization.cpp optimization.h

parsmultistate.cpp parsmultistate.h

pattern.cpp pattern.h

pda.cpp

pdnetwork.cpp pdnetwork.h

pdtree.cpp pdtree.h

pdtreeset.cpp pdtreeset.h

phyloanalysis.cpp phyloanalysis.h

phylonode.cpp phylonode.h

phylosupertree.cpp phylosupertree.h

phylotree.cpp phylotree.h

phylotreesse.cpp phylokernelnew.h

phylotreepars.cpp

pruning.cpp pruning.h

quartet.cpp

split.cpp split.h

splitgraph.cpp splitgraph.h

splitset.cpp splitset.h

stoprule.cpp stoprule.h

superalignment.cpp superalignment.h

superalignmentpairwise.cpp superalignmentpairwise.h

supernode.cpp supernode.h

tinatree.cpp tinatree.h

tools.cpp tools.h

whtest_wrapper.cpp whtest_wrapper.h

lpwrapper.c lpwrapper.h

pllnni.cpp pllnni.h

phylosupertreeplen.cpp phylosupertreeplen.h

phylotesting.cpp phylotesting.h

ecopd.cpp ecopd.h

ecopdmtreeset.cpp ecopdmtreeset.h

graph.cpp graph.h

candidateset.cpp candidateset.h

checkpoint.cpp checkpoint.h

constrainttree.cpp constrainttree.h

MPIHelper.cpp MPIHelper.h

memslot.cpp memslot.h

main/main.cpp

main/phyloanalysis.cpp

main/phyloanalysis.h

main/phylotesting.cpp

main/phylotesting.h

)



if(Backtrace_FOUND)
@@ -553,30 +522,16 @@ if(Backtrace_FOUND) 
  target_link_libraries(iqtree ${Backtrace_LIBRARY})

endif(Backtrace_FOUND)



if (NOT IQTREE_FLAGS MATCHES "nozlib")

    find_package(ZLIB)

endif()



if(ZLIB_FOUND)

  message ("Using system zlib")

  include_directories(${ZLIB_INCLUDE_DIRS})

  target_link_libraries(iqtree ${ZLIB_LIBRARIES})

else(ZLIB_FOUND)

  message ("Using own zlib-1.2.7")

  include_directories("${PROJECT_BINARY_DIR}/zlib-1.2.7" "${PROJECT_SOURCE_DIR}/zlib-1.2.7")

  add_subdirectory(zlib-1.2.7)

  target_link_libraries(iqtree zlibstatic)

endif(ZLIB_FOUND)



if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma")

    if (NOT IQTREE_FLAGS MATCHES "nosse")

        set_target_properties(iqtree ncl lbfgsb whtest sprng vectorclass model PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")

        set_target_properties(iqtree ncl nclextra utils pda lbfgsb whtest sprng vectorclass model alignment tree PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")

    endif()

    set_target_properties(kernelsse pll PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")

	if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")

		set_target_properties(kernelavx pllavx PROPERTIES COMPILE_FLAGS "${AVX_FLAGS}")

		set_target_properties(kernelfma PROPERTIES COMPILE_FLAGS "${FMA_FLAGS}")

        if (IQTREE_FLAGS MATCHES "512")

        if (IQTREE_FLAGS MATCHES "KNL")

            set_target_properties(kernelavx512 PROPERTIES COMPILE_FLAGS "${AVX512_FLAGS}")

        endif()

	endif()
@@ -598,7 +553,7 @@ if (IQTREE_FLAGS MATCHES "libcxx") 
endif()



set(THREAD_LIB "")

if (IQTREE_FLAGS MATCHES "omp")

if (NOT IQTREE_FLAGS MATCHES "single")

	link_directories(${PROJECT_SOURCE_DIR}/lib)

	if (MSVC)

		if (BINARY32)
@@ -612,9 +567,9 @@ if (IQTREE_FLAGS MATCHES "omp") 
		set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -L${PROJECT_SOURCE_DIR}/libmac")

	elseif(CLANG AND WIN32)

        if (BINARY32)

            set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -L${PROJECT_SOURCE_DIR}/lib32 libiomp5md.dll")

            target_link_libraries(iqtree ${PROJECT_SOURCE_DIR}/lib32/libiomp5md.dll)

        else()

            set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -L${PROJECT_SOURCE_DIR}/lib libiomp5md.dll")

            target_link_libraries(iqtree ${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll)

        endif()

#        set(THREAD_LIB "ompstatic")

	endif()
@@ -626,7 +581,7 @@ if (IQTREE_FLAGS MATCHES "omp") 
endif()



# basic linking librararies

target_link_libraries(iqtree pll ncl lbfgsb whtest sprng vectorclass model gsl ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})

target_link_libraries(iqtree pll ncl nclextra utils pda lbfgsb whtest sprng vectorclass model gsl alignment tree ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})



if (NOT IQTREE_FLAGS MATCHES "nosse")

    target_link_libraries(iqtree kernelsse)
@@ -643,7 +598,7 @@ endif() 
# SSE, AVX etc. libraries

if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")

    target_link_libraries(iqtree pllavx kernelavx kernelfma)

    if (IQTREE_FLAGS MATCHES "512")

    if (IQTREE_FLAGS MATCHES "KNL")

        target_link_libraries(iqtree kernelavx512)

    endif()

endif()
@@ -653,7 +608,7 @@ endif() 
set_target_properties(iqtree PROPERTIES OUTPUT_NAME "iqtree${EXE_SUFFIX}")



# strip the release build

if (CMAKE_BUILD_TYPE STREQUAL "Release" AND (GCC OR CLANG)) # strip is not necessary for MSVC

if (CMAKE_BUILD_TYPE STREQUAL "Release" AND (GCC OR CLANG) AND NOT APPLE) # strip is not necessary for MSVC

	if (WIN32)

		ADD_CUSTOM_COMMAND(TARGET iqtree POST_BUILD COMMAND strip $<TARGET_FILE:iqtree>)

	elseif (NOT APPLE)
@@ -682,10 +637,11 @@ install (TARGETS iqtree DESTINATION bin) 
install (FILES "${PROJECT_SOURCE_DIR}/example/models.nex" DESTINATION .)

install (FILES "${PROJECT_SOURCE_DIR}/example/example.phy" DESTINATION .)

install (FILES "${PROJECT_SOURCE_DIR}/example/example.nex" DESTINATION .)

install (FILES "${PROJECT_SOURCE_DIR}/example/example.cf" DESTINATION .)



if (WIN32)

	install (FILES "${BINARY_DIR}/iqtree${EXE_SUFFIX}-click.exe" DESTINATION bin)

	if (EXE_SUFFIX MATCHES "omp" AND MSVC)

	if (NOT IQTREE_FLAGS MATCHES "single" AND MSVC)

        if (BINARY32)

            install(FILES  "${PROJECT_SOURCE_DIR}/lib32/pthreadVC2.dll" DESTINATION bin)

            install(FILES  "${PROJECT_SOURCE_DIR}/lib32/libiomp5md.dll" DESTINATION bin)
@@ -697,7 +653,7 @@ if (WIN32) 
#		install(FILES  "${PROJECT_SOURCE_DIR}/lib/pthreadGC2_64.dll" DESTINATION bin)

	endif()



	if (EXE_SUFFIX MATCHES "omp" AND CLANG)

	if (NOT IQTREE_FLAGS MATCHES "single" AND CLANG)

        if (BINARY32)

            install(FILES  "${PROJECT_SOURCE_DIR}/lib32/libiomp5md.dll" DESTINATION bin)

        else()
@@ -712,7 +668,7 @@ endif() 
##############################################################

include (InstallRequiredSystemLibraries)

set (CPACK_RESOURCE_FILE_LICENSE

     "${CMAKE_CURRENT_SOURCE_DIR}/License.txt")

     "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")

set (CPACK_PACKAGE_VERSION_MAJOR "${iqtree_VERSION_MAJOR}")

set (CPACK_PACKAGE_VERSION_MINOR "${iqtree_VERSION_MINOR}")

set (CPACK_PACKAGE_VERSION_PATCH "${iqtree_VERSION_PATCH}")
@@ -742,8 +698,8 @@ if (BINARY32) 
    set (SYSTEM_NAME "${SYSTEM_NAME}32")

endif()



if (IQTREE_FLAGS MATCHES "512")

    set (SYSTEM_NAME "${SYSTEM_NAME}512")

if (IQTREE_FLAGS MATCHES "KNL")

    set (SYSTEM_NAME "${SYSTEM_NAME}KNL")

endif()



set(CPACK_PACKAGE_FILE_NAME

License.txt

deleted100644 → 0
+0 −340

File deleted.

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README.md

+25 −6
Original line number Diff line number Diff line
@@ -16,7 +16,7 @@ Key features of IQ-TREE 


* __Efficient search algorithm__: Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihood while requiring similar amount of computing time ([Nguyen et al., 2015]).

* __Ultrafast bootstrap__: An ultrafast bootstrap approximation (UFBoot) to assess branch supports. UFBoot is 10 to 40 times faster than RAxML rapid bootstrap and obtains less biased support values ([Minh et al., 2013]).

* __Ultrafast model selection__: An ultrafast and automatic model selection (ModelFinder) which is 10 to 100 times faster than jModelTest and ProtTest. ModelFinder also finds best-fit partitioning scheme like PartitionFinder.

* __Ultrafast model selection__: An ultrafast and automatic model selection (ModelFinder) which is 10 to 100 times faster than jModelTest and ProtTest. ModelFinder also finds best-fit partitioning scheme like PartitionFinder ([Kalyaanamoorthy et al., 2017]).

* __Phylogenetic testing__: Several fast branch tests like SH-aLRT and aBayes test ([Anisimova et al., 2011]) and tree topology tests like the approximately unbiased (AU) test ([Shimodaira, 2002]).
@@ -25,6 +25,8 @@ The strength of IQ-TREE is the availability of a wide variety of phylogenetic mo 
* __Common models__: All [common substitution models](http://www.iqtree.org/doc/Substitution-Models) for DNA, protein, codon, binary and morphological data with [rate heterogeneity among sites](http://www.iqtree.org/doc/Substitution-Models/#rate-heterogeneity-across-sites) and [ascertainment bias correction](http://www.iqtree.org/doc/Substitution-Models/#ascertainment-bias-correction) for e.g. SNP data.

* __[Partition models](http://www.iqtree.org/doc/Complex-Models/#partition-models)__: Allowing individual models for different genomic loci (e.g. genes or codon positions), mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths between partitions.

* __Mixture Models__: [fully customizable mixture models](http://www.iqtree.org/doc/Complex-Models/#mixture-models) and [empirical protein mixture models](http://www.iqtree.org/doc/Substitution-Models/#protein-models) and.

* __Polymorphism-aware models (PoMo)__: <http://www.iqtree.org/doc/Polymorphism-Aware-Models>





IQ-TREE web service

-------------------
@@ -46,19 +48,35 @@ _The average response time is one working day._ 
Citations

---------



To cite IQ-TREE please use:

When using ModelFinder please cite:



* S. Kalyaanamoorthy, B.Q. Minh, T.K.F. Wong, A. von Haeseler, L.S. Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. *Nat. Methods*, 14:587-589. <https://doi.org/10.1038/nmeth.4285>



When performing tree reconstruction please cite:



* L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. *Mol. Biol. Evol.*, 32, 268-274. [DOI: 10.1093/molbev/msu300](http://dx.doi.org/10.1093/molbev/msu300)

* L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. *Mol. Biol. Evol.*, 32, 268-274. <https://doi.org/10.1093/molbev/msu300>



For the ultrafast bootstrap (UFBoot) please cite:



* B.Q. Minh, M.A.T. Nguyen, and A. von Haeseler (2013) Ultrafast approximation for phylogenetic bootstrap. *Mol. Biol. Evol.*, 30:1188-1195. [DOI: 10.1093/molbev/mst024](http://dx.doi.org/10.1093/molbev/mst024)

* D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, and L.S. Vinh (2017) UFBoot2: Improving the ultrafast bootstrap approximation. *Mol. Biol. Evol.*, in press. <https://doi.org/10.1093/molbev/msx281>



When using posterior mean site frequency model (PMSF) please cite:



* H.C. Wang, B.Q. Minh, S. Susko, A.J. Roger (in press) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. *Syst. Biol.* <https://doi.org/10.1093/sysbio/syx068>



When using partition models please cite:



* O. Chernomor, A. von Haeseler, B.Q. Minh (2016) Terrace aware data structure for phylogenomic inference from supermatrices. *Syst. Biol.*, 65:997-1008. <https://doi.org/10.1093/sysbio/syw037>



When using polymorphism-aware models please cite:



* D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, C. Kosiol (2016) Reversible polymorphism-aware phylogenetic models and their application to tree inference. *J. Theor. Biol.*, 407:362-370. <https://doi.org/10.1016/j.jtbi.2016.07.042>



#### Credits and Acknowledgements



Some parts of the code were taken from the following packages/libraries: [Phylogenetic likelihood library](http://www.libpll.org), [TREE-PUZZLE](http://www.tree-puzzle.de), 

[BIONJ](http://dx.doi.org/10.1093/oxfordjournals.molbev.a025808), [Nexus Class Libary](http://dx.doi.org/10.1093/bioinformatics/btg319), [Eigen library](http://eigen.tuxfamily.org/),

[SPRNG library](http://www.sprng.org), [Zlib library](http://www.zlib.net), gzstream library, [vectorclass library](http://www.agner.org/optimize/), [GNU scientific library](https://www.gnu.org/software/gsl/).

[SPRNG library](http://www.sprng.org), [Zlib library](http://www.zlib.net), [gzstream library](http://www.cs.unc.edu/Research/compgeom/gzstream/), [vectorclass library](http://www.agner.org/optimize/), [GNU scientific library](https://www.gnu.org/software/gsl/).





IQ-TREE was partially funded by the [Austrian Science Fund - FWF](http://www.fwf.ac.at/) (grant no. I 760-B17 from 2012-2015 and and I 2508-B29 from 2016-2019) and the [University of Vienna](https://www.univie.ac.at/) (Initiativkolleg I059-N).
@@ -66,6 +84,7 @@ IQ-TREE was partially funded by the [Austrian Science Fund - FWF](http://www.fwf 


[Anisimova et al., 2011]: http://dx.doi.org/10.1093/sysbio/syr041

[Guindon et al., 2010]: http://dx.doi.org/10.1093/sysbio/syq010

[Kalyaanamoorthy et al., 2017]: https://doi.org/10.1038/nmeth.4285

[Minh et al., 2013]: http://dx.doi.org/10.1093/molbev/mst024

[Nguyen et al., 2015]: http://dx.doi.org/10.1093/molbev/msu300

[Shimodaira, 2002]: http://dx.doi.org/10.1080/10635150290069913

alignment/CMakeLists.txt

0 → 100644
+18 −0
Original line number Diff line number Diff line 
add_library(alignment

pattern.cpp

pattern.h

alignment.cpp

alignment.h

alignmentpairwise.cpp

alignmentpairwise.h

maalignment.cpp

maalignment.h

superalignment.cpp

superalignment.h

superalignmentpairwise.cpp

superalignmentpairwise.h

superalignmentpairwiseplen.cpp

superalignmentpairwiseplen.h

)



target_link_libraries(alignment ncl gsl)

alignment.cpp→alignment/alignment.cpp

+979 −198

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