| More docs on the ARB website. See also index of helppages. Last update on 10. Sep 2018 .

Main topics:

- ARB: a Short Introduction
- Glossary

Related topics:

- consensus.ps (Postscript)

# How is the consensus calculated?

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

## OCCURRENCE

### ARB_NT/SAI/Create SAI using../Consensus

### ARB_EDIT4/Properties/Consensus definition

## DESCRIPTION

### What to do with gaps?

If a column contains only gaps the result will be shown as '='.
Define whether to use or to ignore gaps entirely:
If you count gaps and the gap frequency exceeds 'threshold for gaps', the result will be shown as '-'.
If the switch is 'off', the algorithm will virtually remove all gaps. That means if you have a column with two 'A's and 500 gaps the program thinks of 100% 'A'. (If the switch is 'on', the relative number of 'A's would be 2%)

### Simplify using IUPAC

Define whether the most frequent base or the IUPAC code (more then one base) should be shown at the particular position by pressing the respective checkbox after the 'simplify' prompt.
Characters are used for IUPAC encoding only if their frequency exceeds 'threshold for character'.
Example:
If you have 40% 'A', 10% 'C', 40% 'G' and 10% 'T' and 'threshold for character' is set to 20%, the program looks for a iupac code only for 'A' and 'G'.
Note:
The IUPAC codes are displayed after pressing the 'show IUPAC' button.

### Show as upper or lower case?

Define whether the character is displayed in upper or lower case or whether a dot is displayed.
Define upper and lower limit:
If the percentage of a character is above or equal to the upper limit, the character is displayed in upper case.
If the percentage of a character is above or equal to the lower limit and below the upper limit, the character is displayed in lower case.
Otherwise a dot ('.') is displayed.

## NOTES

### None

## EXAMPLES

### None

## WARNINGS

### IUPAC symbols in source sequences are ignored.

## BUGS

### 'consensus.ps (Postscript) ' is broken for more than 10 years now. Seems that nobody ever took a look.