GitHub - isinaltinkaya/ngsAMOVA: Tool for performing AMOVA, Dxy and neighbor joining trees with NGS data

Genotype likelihood framework for Analysis of Molecular Variance with NGS data
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ngsAMOVA: [A]nalysis of [MO]lecular [VA]riance with NGS data

git clone https://github.com/isinaltinkaya/ngsAMOVA.git; cd ngsAMOVA; make

Install dependencies

sudo apt-get install libz-dev liblzma-dev libbz2-dev libcurl4-openssl-dev g++ make

For more examples, please refer to the Documentation

If -f/--formula is not defined, ngsAMOVA will assume input metadata file is ordered and all of its hierarchical levels will be used.

./ngsAMOVA --formula "Individuals ~ Regions/Populations"

Individuals,Regions,Populations
ind1,reg1,pop1
ind2,reg1,pop2
ind3,reg2,pop3
ind4,reg2,pop3
ind5,reg2,pop4

Name		Name	Last commit message	Last commit date
Latest commit History 206 Commits
.github/workflows		.github/workflows
doc		doc
htslib @ e978164		htslib @ e978164
plot		plot
test		test
.gitignore		.gitignore
.gitmodules		.gitmodules
Makefile		Makefile
README.md		README.md
amova.cpp		amova.cpp
amova.h		amova.h
argStruct.cpp		argStruct.cpp
argStruct.h		argStruct.h
bootstrap.cpp		bootstrap.cpp
bootstrap.h		bootstrap.h
dataStructs.cpp		dataStructs.cpp
dataStructs.h		dataStructs.h
dev.h		dev.h
dmat.cpp		dmat.cpp
dmat.h		dmat.h
dxy.cpp		dxy.cpp
dxy.h		dxy.h
em.cpp		em.cpp
em.h		em.h
ibd.cpp		ibd.cpp
ibd.h		ibd.h
io.cpp		io.cpp
io.h		io.h
jgtmat.cpp		jgtmat.cpp
jgtmat.h		jgtmat.h
lookup.cpp		lookup.cpp
lookup.h		lookup.h
metadata.cpp		metadata.cpp
metadata.h		metadata.h
neighborJoining.cpp		neighborJoining.cpp
neighborJoining.h		neighborJoining.h
ngsAMOVA.cpp		ngsAMOVA.cpp
paramStruct.cpp		paramStruct.cpp
paramStruct.h		paramStruct.h
shared.h		shared.h
vcfReader.cpp		vcfReader.cpp
vcfReader.h		vcfReader.h