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The 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), \
[...]
|
tree={string}The tag name of the tree to analyse.
max_brlen={float>0}Branch length threshold: any block with a tree containing at least one branch lenght longer than the given threshold will be filtered out.
file={none|{path}}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={none|gzip|zip|bzip2}Compression format for output file (if file != none).