NAME

reroot - Compute a (new) root for the tree.

SYNOPSIS

reroot [OPTIONS] tree-file

DESCRIPTION

This program reroots the trees in <treefile> on an selected edge.

The default is to output a random rerooting, but you can also choose to give the edge to put the root on, or an outgroup, or even all possible rootings.

Output is written to stdout unless the exhaustive rooting is chosen. Then -o is giving the prefix for filenames to use and the results are written to <prefix>_<n>.tree, where <n> is the node number of the head of the edge.

Warning! In the current implementation all time/length info is lost.

OPTIONS

--help

Display help

-V, --version

Print version and exit

-S, --read-tree-from-stdin

read tree from STDIN (no <tree-file>)

-f, --input-format prime|inputxml

The input format. Default is prime

-e, --exhaustive

Do all possible rootings

-o, --output-file-prefix file-prefix

The stem for filenames

-n, --node-index INT

Reroot tree at edge leading to node

-g, --outgroup STRING

Root tree at smallest subtree containing the leaves listed in a commaseparated arguments

EXIT STATUS

0

Successful program execution.

1

Some error occurred

URL

The prime-phylo home page: http://prime.sbc.su.se

SEE ALSO

primeDTLSR(1), primeDLRS(1), primeGEM(1), chainsaw(1), reconcile(1), showtree(1), tree2leafnames(1), treesize(1)