TreeFilter (experimental) filters blocks based on their associated trees. Currently, filter is only performed based on the branch lengths.
maf.filter= \ [...], TreeFilter( \ tree=BioNJ, \ max_brlen=0.01, \ file=data.trash_tree.maf.gz, \ compression=gzip), \ [...]
The tag name of the tree to analyse.
Branch length threshold: any block with a tree containing at least one branch lenght longer than the given threshold will be filtered out.
An optional file were removed alignment parts will be stored, in the MAF format. This can be helpful for visual inspection and fine tuning of the filter parameters.
Compression format for output file (if file != none).