About

This is the manual for FineSTRUCTURE Version 2.9.0pre . FineSTRUCTURE is software to perform population assignment using large numbers of densely sampled genomes, including both SNP chips and sequence data. This version greatly simplifies its use, removing the complex pipeline and allowing very simple use for small datasets, and reasonably simple integration with High Performance Computing (HPC) machines.

See www.paintmychromosomes.com for the most up to date information. The correct reference is:

• Inference of population structure using dense haplotype data, Daniel Lawson, Garrett Hellenthal, Simon Myers, and Daniel Falush, 2012. PLoS Genetics, Vol. 8(1): e1002453,

which contains the motivation and justification behind the method. Similar in concept to STRUCTURE, fineSTRUCTURE assigns individuals to populations using a model for the expected variability. The advantage of our approach is that very large numbers of SNPs (Single Nucleotide Polymorphisms) can be used and linkage disequilibrium can be efficiently exploited. To achieve this the computation is split into a painting step and a population inference step.

This software is currently only available for Linux and Unix compatible operating systems (such as Mac). To use it with Windows you will need cygwin. Version 0 is available for Windows, but its use is strongly discouraged due to the inherent difficulty of running a genomics pipeline via graphical interfaces. The version described in this manual is command-line only; Refer to the Version 0 manual for information about the GUI.

This software is Beta: please report all bugs to the author.