GitHub - manlug/popPhylABC: Scripts used for ABC analysis with homo- and heterogeneity in Migration rates or/and Effective population sizes

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Scripts used for ABC analysis with homo- and heterogeneity in Migration rates or/and Effective population sizes

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Name		Name	Last commit message	Last commit date
Latest commit History 76 Commits
data_popPhylABC		data_popPhylABC
divergence_fst		divergence_fst
example		example
figures		figures
mscalc		mscalc
msnsam		msnsam
revisions		revisions
tables		tables
README		README
croux.pdf		croux.pdf
popPhyl2ABC_v2.py		popPhyl2ABC_v2.py
priorgen.py		priorgen.py

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Datasets from the popPhyl project:
https://lc.cx/4Eid

Converting fasta files into input for ABC analysis:
popPhyl2ABC_v2.py

This code depends on the C++ library libsequence by calling polydNdS to get synonymous positions.
An incompatibility had been reported with version of libsequence >2.0 !!!
https://github.com/molpopgen/analysis


To compile mscalc, the calculator of statistics:
gcc *.c -lm -o mscalc

To compile msnsam, the coalescent simulator (Ross-Ibarra et al, 2008):
./clms

The following programs have to be linked to your bin/ :
	mscalc
	priorgen.py
	msnsam
	popPhyl2ABC_v2.py
	polydNdS