RapGreen reconciliation command line documentation

NAME:

    - RAP-Green v1.0 -

---

SYNOPSIS:

    java -jar RapGreen.jar command args

---

MAIN OPTIONS:

    -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)

---

CONFIDENTIAL OPTIONS:

    -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)

---

DEPRECATED OPTIONS:

    -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