1 Changes from Version 0
2 How to use this software
3 Overview of FineSTRUCTURE and the help system
 3.1 Information about the processing pipeline
 3.2 Basic Help for ‘automatic mode’
4 Detailed help
 4.1 Information on Input formats
 4.2 Help on how the computation is performed
 4.3 Help on the output files created
 4.4 Help on specific parameters
 4.5 Accessing FineSTRUCTURE, ChromoCombine and ChromoPainter directly
 4.6 List of all parameters
5 ChromoPainter
6 ChromoCombine
7 FineSTRUCTURE
8 Computational considerations
9 Greedy finestructure
10 Job submission in qsub and related environments
11 Provided scripts
 11.1 makeuniformrecfile.pl
 11.2 convertrecfile.pl
 11.3 chromopainter2chromopainterv2.pl
 11.4 phasescreen.pl
 11.5 phasesubsample.pl
 11.6 plink2chromopainter.pl (PLINK)
 11.7 impute2chromopainter.pl (SHAPEIT format)
 11.8 beagle2chromopainter.pl (BEAGLE format)
 11.9 msms2cp.pl (MSMS and MS output format)
12 Potential pitfalls
13 Examples
 13.1 Simple and quick example
 13.2 Involved example with few SNPs and individuals
 13.3 HGDP example, including downloading and processing.
14 Additional comments