RapGreen reconciliation command line documentation
Jean-François edited this page Aug 20, 2020
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- RAP-Green v1.0 -
java -jar RapGreen.jar command args
-g gene_tree_file
The input gene tree file
-s species_tree_file
The input species tree file
-nhx gene_tree_nhx_file
The output tree file (annotated with duplications) in NHX format, strongly recommended
-stats gene_tree_file
The output scoring statistic file
-gt gene_threshold
The support threshold for gene tree branch collapse (optional, default 80.0)
-st species_threshold
The length threshold for species tree branch collapse (optional, default 10.0)
-pt polymorphism_threshold
The length depth threshold to deduce to polymorphism, allelism ... (optional, default 0.05)
-os species_tree_file
The output species tree file (limited to gene tree species)
-or reconciled_tree_file
The output reconciled tree file (consensus tree, with reductions and losses)
-invert
Activate this option if your taxa identifier is in front of the sequence identifier
-pipe
Activate this option if your taxa identifier contains pipes instead of underscores
-start starting_index
The starting index (0 default), if the gene tree input is a directory
-end ending_index
The ending exclusive index (directory size default), if the gene tree input is a directory
-rerooted gene_tree_file
The simple unannotated rerooted gene tree file
-rerootedSpecies gene_tree_file
The simple unannotated rerooted gene tree file, with only species on the leaf (for supertrees for example)
-outparalogous
Add outparalogous informations in stats file
-prefix prefix taxa
A prefix to be translated to a specific taxa, in sequence name.
-k k_level
The k-level of the subtree-neighbor measure (optional, default 2)
-idupw i_duplication_weight
The weight of intersection duplication in functional orthology scoring (0.0 for maximum weight, 1.0 for no weight, optional, default 0.90)
-tdupw t_duplication_weight
The weight of topological duplication in functional orthology scoring (0.0 for maximum weight, 1.0 for no weight, optional, default 0.95)
-specw speciation_weight
The weight of speciation in functional orthology scoring (0.0 for maximum weight, 1.0 for no weight, optional, default 0.99)
-ultraw ultraparalogy_weight
The weight of an ultraparalogy node in functional orthology scoring (0.0 for maximum weight, 1.0 for no weight, optional, default 0.99)
-distw distance_weight
The weight of evolutionary distance in functional orthology scoring (0.0 for maximum weight, 1.0 for no weight, optional, default 0.10)
-og gene_tree_file
The output tree file (annotated with duplications on the label)
-phyloxml gene_tree_phyloxml_file
The output tree file (annotated with duplications) in phyloXML format
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