Google
More docs on the ARB website.
See also index of helppages.
Last update on 30. Nov 2022 .
Main topics:
 Related topics:

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 ´Node Display Setup (NDS)´, 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

 

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