csubst site --mode

[kfuku52]

• --mode intersection: default. Visualizing combinatorial substitutions of branches specified by --branch_id. Generating 1 pse.
• --mode total: Color intensity according to the number of all amino acid substitutions in the branches specified by --branch_id.
• --mode each: Visualizing all amino acid substitutions in individual branches specified by --branch_id. Generating N pse.
• --mode all: Visualizing all amino acid substitutions in all individual branches. Ignoring --branch_id. Generating N pse.
• --mode clade: Visualizing all amino acid substitutions in individual branches of the clade specified by --branch_id, which should accept only one argument with this option. Generating N pse.
• --mode lineage: Visualizing all amino acid substitutions in individual branches between an ancestor and an descendant specified as --branch_id ANC,DES. Substitutions are rainbow-colored in 1 pse.

[kfuku52]

--mode lineage can change the colors depending on another option (--color {stratigraphy,count}) to specify which of ancestor-descendant stratigraphy and the number of site-wise substitutions should be displayed.

[kfuku52]

Another option is to utilize arithmetic operators like +, -, *, and /, to allow a more flexible operations, with --mode set,value to distinguish a python's set()-like operation and a more direct posterior probability calculation (or, --ml_anc does this job in place of --mode set,value).