PASTML infers ancestral states on a phylogenetical tree with annotated tips.

usage: PASTML -a ANNOTATION_FILE -t TREE_NWK [-m MODEL] [-o OUTPUT_ANNOTATION_FILE] [-n OUTPUT_TREE_NWK] [-s SCALING_ON_OFF] [-I KEEP_INTERNAL_NODE_IDS_ON_OFF] [-f CHAR_FREQUENCES]

required arguments:
   -a ANNOTATION_FILE                  path to the annotation csv file containing tip states
   -t TREE_NWK                         path to the tree file (in newick format)

optional arguments:
   -o OUTPUT_ANNOTATION_FILE           path where the output annotation csv file containing node states will be created
   -n OUTPUT_TREE_NWK                  path where the output tree file will be created (in newick format)
   -m MODEL                            state evolution model (JC or F81)
   -s SCALING_ON_OFF                   branch length scaling on (T, by default) or off (F)
   -I KEEP_INTERNAL_NODE_IDS_ON_OFF    keep internal node ids from the input tree: T (true) or F (false)

