Simultaneous estimation of methylation levels

MLML is a useful tool to simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels from BS-seq, oxBS-seq and TAB-seq experiments. It generates consistent estimates across experiment types.

System requirements

64-bit machine, GCC version >= 4.1, and GSL version 1.15 available here.


MLML is now a part of the MethPipe package. Please see the MethPipe homepage for installation details.

Example usage

Click to download test data to give a try: test data (14KB)

If only BS-seq data (FILE_BS) and Tab-seq data (FILE_TAB) are available, run

$ mlml -v -u FILE_BS -h FILE_TAB -o OUTPUT_FILE

The program will output estimates to OUTPUT_FILE and print summary statistics to screen.

For more examples and detailed information about options and usage, please check the manual in MethPipe package.