svr_get_ali_and_tree

Get alignments and trees corresponding based on a set of gene IDs.

------

Example:

    svr_get_ali_and_tree -d Output < PEGs

andirectory of output (Output will be created, if it does not already exist). There will be one subdirectory for every input PEG. That directory will contain a set of files that will include the alignment, the tree, and the HTML files to display each.

------

    The input should be a file; each line in the file should contain a single PEG ID.

Command-Line Options

-d OutputDirectory

-a anno Use the annotator's Seed

-ppseed Use the PubSEED

-nocollapse [ do not collapse the tree -- show all sequences ]

Output Format

POD ERRORS

Hey! The above document had some coding errors, which are explained below:

Around line 68:

You forgot a '=back' before '=head2'