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)

prime-phylo 1.0.11                                13 Mar, 2012                                         reroot(1)