| More docs on the ARB website. See also index of helppages. Last update on 27. Jun 2017 .

Main topics:

- ARB: a Short Introduction
- Glossary
- How to start ARB_EDIT4

Related topics:

- PT_SERVER: What Why and How

# Old aligner from ARB_EDIT

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

## OCCURRENCE

### ARB_EDIT4/Edit/Old aligner from ARB_EDIT

## DESCRIPTION

### Aligns or realigns selected sequence with the database sequences. The most similar database sequences are found, and the new sequence is aligned with these according to primary and secondary structure similarity.

### Select whether to align the sequence of the selected species or all marked species.

### Select whether to align versus an explicit reference or the nearest relative reported by the PT_SERVER.

### The used relatives may be marked by checking 'Mark sequences found by the pt_server'.

### Press <GO>

## NOTES

### Marking the closest relatives allows manual optimization of the alignment of the new species with its closest relatives.

## EXAMPLES

### None

## WARNINGS

### The aligner version available with the present package often does not properly align short partial sequences.

## BUGS

### The aligner needs lots of computer memory, sometimes more than you have. In this case it may not align some sequences.

### The aligner does not align the last 3-6 bases of short sequences correctly. Look at the end of your sequences.