search

millanek / fineRADstructure

A package for population structure inference from RAD-seq data
https://www.milan-malinsky.org/fineradstructure
Other
31 stars 7 forks source link

readme

fineRADstructure

Publication:
Malinsky, M., Trucchi, E., Lawson, D. J. & Falush, D. (2018) RADpainter and fineRADstructure: Population Inference from RADseq Data. Molecular Biology and Evolution 35, 1284–1290. doi: https://doi.org/10.1093/molbev/msy023

Quickstart:

Requirements:

Assuming that you are in a Linux/UNIX like environment, you need:

  1. a) On Linux/Unix a reasonably newish version of the gcc compiler (gcc 4.6.2 and onwards work fine)
  2. b) Mac/Apple users need to have the Command Line Tools installed
  3. GNU Scientific Development Library, (libgsl0-dev and libgsl0 in Ubuntu, gsl-devel in OpenSUSE)

Installation:

Briefly: ./configure make

This package includes two exacutables: RADpainter and fineSTRUCTURE

Usage:

  1. Calculate the co-ancestry matrix: ./RADpainter paint INPUT_RAD_FILE.txt
  2. Assign individuals to populations: ./finestructure -x 100000 -y 100000 -z 1000 INPUT_RAD_FILE_chunks.out INPUT_RAD_FILE_chunks.mcmc.xml
  3. Tree building: ./finestructure -m T -x 10000 INPUT_RAD_FILE_chunks.out INPUT_RAD_FILE_chunks.mcmc.xml INPUT_RAD_FILE_chunks.mcmcTree.xml

Further information:

Detailed instructions are available on my personal homepage. Please also read the publication.

RADpainter was written by Milan Malinsky (millanek@gmail.com) and fineSTRUCTURE was written by Daniel Lawson (dan.lawson@bristol.ac.uk)