root

usage: micca root [-h] -i FILE -o FILE [-m {midpoint,outgroup}]
                [-t TARGETS [TARGETS ...]]

micca root reroot the input tree:

* at the calculated midpoint between the two most distant tips of the
tree (--method midpoint);

* with the outgroup clade containing the given taxa (leaf nodes),
i.e. the common ancestor of the outgroup (--method outgroup).

optional arguments:
-h, --help            show this help message and exit

arguments:
-i FILE, --input FILE
                        input FASTA file (required).
-o FILE, --output FILE
                        output MSA file in FASTA format (required).
-m {midpoint,outgroup}, --method {midpoint,outgroup}
                        rooting method (default midpoint).
-t TARGETS [TARGETS ...], --targets TARGETS [TARGETS ...]
                        list of targets defining the outgroup (required for
                        the outgroup method).

Examples

Midpoint rooting:

    micca root -i input.tree -o input_rooted.tree

Rooting with outgroup:

    micca root -i input.tree -o input_rooted.tree -m outgroup DENOVO1 DENOVO2