search

mikolmogorov / maf2synteny

A tool for recovering synteny blocks from multiple alignment
Other
29 stars 7 forks source link

-b parameter explanation #7

Open aminakur opened 1 year ago

aminakur commented 1 year ago

Could you please elaborate on the -b parameter usage? -b block_sizes comma-separated list of synteny block scales [default = 5000] What is a synteny block scale and how to find an optimal one for a particular analysis?

mikolmogorov commented 1 year ago

I suggest reading the Genome Research paper which have the algorithm description. There is no definite algorithm for choosing synteny block scale, but the default setting should work fine in most cases. If the particular parts of the paper are unclear - will be happy to help!