INTRODUCTION
fastGEAR is a software for analysing sequence alignments, and it has been described in a paper:
Mostowy, R., Croucher, N.J., Andam, C.P., Corander, J., Hanage, W.P. and Marttinen, P. (2016). Analysis of recent and ancestral recombination reveals high-resolution population structure in Streprococcus pneumoniae. Submitted.


COPYRIGHT NOTICE
 2016 Authors

fastGEAR can be downloaded from https://users.ics.aalto.fi/~pemartti/fastGEAR/ and used freely for academic purposes. If you use fastGEAR, please cite the paper specified above. Furthermore, you can modify and redistribute the source code on the condition that the original citation and this notice accompany the modified version.

fastGEAR comes with no warranties whatsoever. The user alone is responsible for results obtained with fastGEAR.

We note that fastGEAR has been tested extensively with synthetic data sets and using empirical genome alignments in order to verify the basic correctness of the algorithm. However, if you observe suspicious behaviour or unexpected crashes, please notify us by sending e-mail to the address pekka 'dot' marttinen 'at' aalto 'dot' fi


GETTING STARTED WITH THE SOURCE CODE
Have a look at "testFastGear.m", and try running it.