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# Column Statistic (Prototype)

- OCCURRENCE
- DESCRIPTION
- NOTES
- WARNINGS
- BUGS
- Detailed column statistic

## OCCURRENCE

### ARB EDITOR

## DESCRIPTION

### Highlites unlikely bases in an alignment using the maximum likelihood technique. As soon as the go button is pressed, the selected tree (by ARB_NT) and all marked sequences are read. Then the relative likelihood for each base is calculated and transformed to a number between 0 and 9. This number is translated into a color, using the colors 'RANGE 0 ... RANGE 9'. The higher the number, the more unlikely a particular base. You may improve the output by selecting a valid column statistic, which holds information about column dependent rates and base frequencies.

## NOTES

### The colors are not set correctly. Please set different 'CS' colors <Props:Sequences: Colors and Fonts> and save them. Without a powerfull computer only a small number of sequences can be viewed. The program assumes that your tree is correct.

## WARNINGS

### This is only a prototype, don't expect something perfect. All sequences which should be analyzed should be marked and in the tree shown by ARB_NT !!!!!

## BUGS

### The colors are not set correctly by default. The program can only be started once.

## Detailed column statistic

### This special mode displays 4 rows below the sequence containing the likelihood of each base character.

### Each row consists of two rows of digits displayed in the same color (which actually is the color normally used for displaying the appropriate base character). The upper of these two rows is the first, the lower the second digit of the likelihood. [You may like to use the cursor to simplify reading]

    Special character used:
    -----------------------
    SPACE   = likelihood is 20%
    ^       = likelihood is 100%
    ?       = can't determine likelihood for that column

### Background colors used: ----------------------- Normally the normal background color is used.

### If a column has a significant likelihood for one base character (or for the sum of two base characters), all four rows are displayed in color 'Range 0'.

### [significance is 90% (hardcoded) - will be made utilizable soon]

### The single (or two) base character(s) responsive for the significance will be displayed in colors 'Range 1' to 'Range 8' (the higher the Range-number is, the higher is the likelihood)