A Python script that implements the classifier Trendsetter of Mughal and DeGiorgio (2019) for classifying genomic regions as neutral, hard sweep, or soft sweep using the spatial distribution of summary statistics around a test site.

Results of genome scans for selective sweeps using Trendsetter as applied to seven 1000 Genomes Project populations in Mughal and DeGiorgio (2019).
[Click to download scan results]

Please cite the following manuscript if using this software:
MR Mughal, M DeGiorgio (2019) Localizing and classifying adaptive targets with trend filtered regression. Molecular Biology and Evolution 36:252-270.

[Click to download manual]
[Click to download software (300 MB download including example data)]

On a UNIX system, extract the compressed files using the command
tar -xzvf trendsetter.tar.gz
Change directory to trendsetter using a command such as
cd trendsetter
The script will be located in the trendsetter directory

Software history
May 11, 2018 - Uploaded version 1.0 of the software and manual
August 31, 2018 - Updated software to include classifier calibration