GitHub - danjlawson/fineRADstructure: A package for population structure inference from RAD-seq data

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Name		Name	Last commit message	Last commit date
Latest commit History 54 Commits
config		config
AUTHORS		AUTHORS
COPYING		COPYING
ChangeLog		ChangeLog
FinestructureLibrary.R		FinestructureLibrary.R
INSTALL		INSTALL
Makefile.am		Makefile.am
Makefile.in		Makefile.in
NEWS		NEWS
README		README
Stacks2fineRAD.py		Stacks2fineRAD.py
aclocal.m4		aclocal.m4
configure		configure
configure.ac		configure.ac
data.cpp		data.cpp
data.h		data.h
fineRADstructurePlot.R		fineRADstructurePlot.R
fines.cpp		fines.cpp
fines.h		fines.h
finesfunctions.cpp		finesfunctions.cpp
finesfunctions.h		finesfunctions.h
fsxml.cpp		fsxml.cpp
fsxml.h		fsxml.h
gzstream.cpp		gzstream.cpp
gzstream.h		gzstream.h
hapsFromVCF.cpp		hapsFromVCF.cpp
hapsFromVCF.h		hapsFromVCF.h
inf1.cpp		inf1.cpp
inf1.h		inf1.h
infadmixture.cpp		infadmixture.cpp
infadmixture.h		infadmixture.h
infextract.cpp		infextract.cpp
infextract.h		infextract.h
infextract2.cpp		infextract2.cpp
infextract2.h		infextract2.h
infextract3.cpp		infextract3.cpp
infextract3.h		infextract3.h
infextract4.cpp		infextract4.cpp
infextract4.h		infextract4.h
infextract5.cpp		infextract5.cpp
infextract5.h		infextract5.h
infmcmc.cpp		infmcmc.cpp
infmcmc.h		infmcmc.h
node.cpp		node.cpp
node.h		node.h
paintSql.cpp		paintSql.cpp
paintSql.h		paintSql.h
rng.cpp		rng.cpp
rng.h		rng.h
safegetline.cpp		safegetline.cpp
safegetline.h		safegetline.h
sampleLD.R		sampleLD.R
state.cpp		state.cpp
state.h		state.h
tagPainter.cpp		tagPainter.cpp
tagPainter.h		tagPainter.h
utils.cpp		utils.cpp
utils.h		utils.h

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README FOR fineRADstructure

For detailed instructions see http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html

A manuscript to cite has been published in MBE: https://doi.org/10.1093/molbev/msy023

1. REQUIREMENTS

Assuming that you are in a Linux/UNIX like environment, you need:
1. an up-to-date version of the gcc compiler, e.g. "gcc (Ubuntu 4.4.3-4ubuntu5) 4.4.3"
2. GNU Scientific Development Library, (libgsl0-dev and libgsl0 in Ubuntu, gsl-devel in OpenSUSE) 
3. Mac/Apple users need to have the Command Line Tools installed

There are probably other requirements which are present on most systems by default.  

2. INSTALLATION

Briefly:

./configure
make

3. FURTHER INFORMATION

This package includes two exacutables: RADpainter and fineSTRUCTURE

RADpainter was written by Milan Malinsky (milan.malinsky@unibas.ch) and fineSTRUCTURE was written by Daniel Lawson (dan.lawson@bristol.ac.uk)