Documentation read from 04/17/2019 22:07:26 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_get_ali_and_tree.



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



    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


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

Around line 68:

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