#Please insert up references in the next lines (line starts with keyword UP)
UP      arb.hlp
UP      glossary.hlp
UP      treeadm.hlp

#Please insert subtopic references  (line starts with keyword SUB)
#SUB    subtopic.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE           Export tree to file

OCCURRENCE      ARB_NT/Tree admin/Export

DESCRIPTION     Writes a tree to file in Newick format

                Press the 'EXPORT' button to display the 'TREE SAVE' window.

                Select a tree file from the 'Directories and Files' subwindow or
                type the file name to the 'FILE NAME' subwindow.

        NEWICK TREE FORMAT

               Nodetype

                      Species ID

                              This is the traditional format using species IDs as leaf names.

                      NDS

                              This uses the current NDS tree settings as leaf names,
                              i.e. this mode can be used for EXPORT ONLY!
                              (until #774 gets implemented).

                              The "truncated" NDS mode respects the WIDTH entry in LINK{props_nds.hlp},
                              as done by the arb tree display.
                              This was the hardcoded behavior until arb-7.0.

                              The newer "untruncated" NDS mode ignores the WIDTH field and
                              always exports complete field contents.

                              Group names are now as well generated via NDS in NDS mode.
                              To export plain group names, use a group NDS with WIDTH=0 and
                              ACI='taxonomy(1)' (which is the current default).

               Label quoting

                    choose whether and how to quote names for leafs and/or groups.
                    Quoting names may be necessary to ensure other software is able
                    to read the generated tree files.

               Replace problem chars

                    if checked, problematic characters in labels will be replaced (currently "()[]:;," plus
                    used quote, if any).

               Save group names

                    if marked, groupnames (taxonomy) are written to the tree file.

               Save branch lengths

                    if marked, branchlengths are written to the tree file.

               Save bootstraps

                    if marked, bootstraps are written to the tree file.

        ARB_XML TREE FORMAT

                Simple XML Format (export only; experimental)

                Hide folded groups

                     If checked, folded groups will be exported as terminal node. Otherwise
                     group contents will be written into tree file.


NOTES           If you select both 'Save group names' and 'Save bootstraps', other programs may be
                unable to load the tree or at least unable to interpret the bootstrap values correctly.

                If a suffix is displayed in or typed to the 'SUFFIX' subwindow,
                only the corresponding filenames will be displayed.
                The suffix is automatically appended to the filename typed
                to the 'File Name' subwindow.

                The different export types cause the suffix to change:

                    - '.tree' for normal newick
                    - '.ntree' for newick using NDS
                    - '.xml' for xml 

SECTION         Keeled groups

                ARB will refuse to store LINK{keeled_groups.hlp} into a newick file.

                To work around that restriction either
                  - uncheck 'Save group names' or
                  - read about howto fix keeled groups.

WARNINGS        Tree data written with the 'NDS' option cannot be
                reimported to the database without data loss!

                It's possible to reload such a tree, but it's leafs
                will not be linked to the correct species.

BUGS            No bugs known