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Last update on 25. Nov 2018 .
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Alignment Administration

OCCURRENCE

ARB_NT/Sequence/Admin

ARB_MERGE/Check alignments/MODIFY

 

DESCRIPTION

This module allows handling and modification of 'alignments' (see ´Glossary´).

Select an alignment from the 'Alignments' subwindow
Define the type of sequences (DNA, RNA, protein):
Press the <Type of Sequences> button and choose from the displayed menu.
Set protection:
Press the <Default Write Protection> button and choose from the displayed menu.
Press the respective buttons to perform further functions:
DELETE:     Delete an alignment and its sequence data
RENAME:     Rename an alignment
CREATE:     Create a new alignment (no data)
COPY:       Copy an alignment
CHECK LEN:  Find the longest sequence and set the
            'Maximum Seq. Length' displayed in the
            corresponding subwindow
FORMAT:     Append '.' to sequences up to 'Maximum Seq.
            Length'.
Auto format: Whether to ask, format or skip w/o asking
             whenever an unformatted alignment is detected.
 

NOTES

Some functions require setting a protection level equal to or higher than that of the 'alignment'.

There is one special alignment called "ali_genom" used for full genome sequences. You can't format that alignment because it is necessary to ensure that it's alignment positions match those used in the gene entries. For the same reason you should never ever put any gap into that alignment.

 

EXAMPLES

None

 

WARNINGS

Be careful when deleting or changing the name of an alignment while other programs are using it (eg. parsimony programs ..)

 

BUGS

No bugs known