2.1.2 SelectOrphans: keep only block with the specified species

The SelectOrphans filter allows to discard all block with species out of the specified range. This is typically used to extract blocks with no homolog ("orphan").

Synopsis:

maf.filter=                                 \
    [...],
    SelectOrphans(                          \
        species=(species1, species2, etc),  \
        strict=yes,                         \
        remove_duplicates=yes),             \
    [...]

Arguments:

species=(species1, species2, etc)

A coma separated, within parentheses, list of species. All block containing at least one species outside this list will be discarded.

strict=yes/no

If set to yes, only block containing at least one sequence from each species in the selection will be kept.

remove_duplicates=yes/no

If set to yes, only keep blocks for which only one sequence for each species is present. Blocks with paralogous sequences in at least one species will therefore be discarded.