2.3.2.5 Filter blocks based on their associated trees

The TreeFilter (experimental) filters blocks based on their associated trees. Currently, filter is only performed based on the branch lengths.

Synopsis:

maf.filter=                                 \
    [...],
    TreeFilter(                             \
        tree=BioNJ,                         \
        max_brlen=0.01,                     \
        file=data.trash_tree.maf.gz,        \
        compression=gzip),                  \
    [...]

Arguments:

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).