Repository for all project code. This project aims to explore patterns of population structure in field isolates of the green alga Chlamydomonas reinhardtii.
Requirements:
bedtools v2.26.0 - https://github.com/arq5x/bedtools2
GATK v3.5 - https://software.broadinstitute.org/gatk/
EMBOSS:6.6.0.0 - http://emboss.sourceforge.net
fineSTRUCTURE - https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure_info.html
hmmIBD - https://github.com/glipsnort/hmmIBD
kentUtils - https://github.com/ENCODE-DCC/kentUtils
MEGA - https://www.megasoftware.net
PopART - http://popart.otago.ac.nz/index.shtml
STRUCTURE - https://web.stanford.edu/group/pritchardlab/structure.html