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# User Defined Distance Matrix

- OCCURRENCE
- DESCRIPTION
- NOTES
- BUGS

## OCCURRENCE

### ARB_DIST

## DESCRIPTION

### Allows the user to define distances between different bases. E.g. An A-T should get a smaller difference as an A-G, so the corresponding matrix elements should be set to 1.0 and 2.0.

## NOTES

### Before the algorithm starts, all matrix values will be multiplied by a factor, so that the average matrix value (except the diagonal) gets a value of one !!!

### To save a user matrix use <Properties/Save Properties> menu item.

## BUGS

### Works only with some distance corrections:

    none    similarity      jukes_cantor

### Works only with dna

### If enabled only ACGTU/GAPS bases are calculated.