| More docs on the ARB website. See also index of helppages. Last update on 24. Jun 2017 .

Main topics:

- ARB: a Short Introduction
- Glossary
- Protection Level

Related topics:

- Insert / Delete Column

# Alignment Administration

- OCCURRENCE
- DESCRIPTION
- NOTES
- EXAMPLES
- WARNINGS
- BUGS

## OCCURRENCE

### ARB_NT/Sequence/Admin

## 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
    SEQ REMARK: Add a remark field to the sequence of the selected SAI
    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'.

### Asterisks indicate functions which are not available with the 'ALIGNMENT CONTROL' functions of the 'MERGE TWO DATABASES' tool.

### 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