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Last update on 25. Nov 2018 .
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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
(Export only!) This uses the current NDS tree settings as leaf names.
Save branch lengths
if marked, branchlengths are written to the tree file.
Save bootstraps
if marked, bootstraps are written to the tree file.
Save groupnames
if marked, groupnames (taxonomy) are written to the tree file.
Name 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 names will be replaced (currently "()[]:;," plus used quote, if any)

ARB_XML TREE FORMAT

Simple XML Format (can't load yet)
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 groupnames' 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 file names will be displayed. The suffix is automatically appended to the file name 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

 

Keeled groups

ARB will refuse to store ´Keeled groups´ 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