A tool for recovering synteny blocks from multiple alignment
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README.md

README.md

maf2synteny

A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat)

This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]

Install

make

Usage

Usage: maf2synteny [-o out_dir] [-s simpl_params] [-m block_sizes] maf_file

positional arguments: maf_file path to maf file

optional arguments: -o out_dir path to the output directory [default = .] -s simpl_params path to a file with simplifcation parameters [default = not set] -b block_sizes comma-separated list of synteny block scales [default = 5000]

Default simplification parameters:

10, 10
30, 100
50, 5000
100, 7000
500, 10000
1500, 50000
5000, 100000
10000, 500000
50000, 1000000