GitHub - arklumpus/rapidNJ-library: Fast implementation of the Neighbour-Joining method for phylogenetic inference

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Fast implementation of the Neighbour-Joining method for phylogenetic inference

GPL-2.0 license

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Name		Name	Last commit message	Last commit date
Latest commit History 17 Commits
bin		bin
lib		lib
obj		obj
src		src
test_data		test_data
LICENSE		LICENSE
Makefile		Makefile
README		README
createDnaDataPhylip.py		createDnaDataPhylip.py
msvc2012.sln		msvc2012.sln
msvc2012.vcxproj		msvc2012.vcxproj
msvc2012.vcxproj.filters		msvc2012.vcxproj.filters
recursive		recursive
vcvars32.sh		vcvars32.sh
vcvars64.sh		vcvars64.sh

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This is a fork of somme/rapidNJ, modified to produce a static library rather than an executable.

Compilation:
Dependencies: C++

On Linux and Mac run "make" from the root directory. Tip use "make -j" to comple on multiple cores

Windows: Use Visual studio or cygwin to compile. The scripts vcvars32.sh or vcvars64.sh show an example on how to compile the binaries using cygwin  commandline and a visual studio compiler 

Installation:
Copy binaries from "./bin" to a suitable location.

Version 2.3.2:
-Fixed bug in bootstrap algorithm which caused the bootstrap values to be lower than the true value in most cases.
-Fixed bug that caused the last two branches to have the wrong distance.

For all publications and documentation see: https://birc.au.dk/software/rapidnj/

Pulication list:
https://users-birc.au.dk/~cstorm/software/rapidnj/papers/SimonsenOthers2008_WABI.pdf
https://users-birc.au.dk/~cstorm/software/rapidnj/papers/SimonsenOthers2011_CCIC.pdf
https://users-birc.au.dk/~cstorm/software/rapidnj/papers/SimonsenPedersen2011_SAC.pdf

Contact:
Martin Simonsen - somme89@gmail.com