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The Subset filter allows to filter sequences for each block by keeping only a selection of species.
maf.filter= \
[...],
Subset( \
species=(species1, species2, etc), \
strict=yes, \
keep=no, \
remove_duplicates=yes), \
[...]
|
species=(species1, species2, etc)A coma separated, within parentheses, list of species. Only sequences corresponding to the selected species will be kept. Block without sequences from the selection will be discarded.
strict=yes/noIf set to yes, only blocks containing at least one sequence from each species in the selection will be kept.
keep=yes/noIf strict is set to yes, tells if additional sequences should be kept in the block, or remove so that the output blocks only contain species from the selection.
remove_duplicates=yes/noIf 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.