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# Matrices, Masks, Profiles V1.0

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

## OCCURRENCE

### ARB_NT/Tree/Dist Matrix V 1.0

## DESCRIPTION

### This tool allows to calculate distance and similarity matrices for the marked species. Conservation profiles can be established and used as filters for column selection by other programs.

1. Selection of columns:
   Select part of the alignment to analyze by typing first and last column numbers after the 'start at column:' and 'stop at column:' prompts, respectively, and press 'Return' on the keyboard.
   Select minimum and maximum similarities for the individual columns to be included for similarity or distance matrix calculation by typing the values (50 means the most frequent base at a particular position is shared by at least 50% of all marked sequences (species)) after the 'minimum similarity:' and 'maximum similarity:' prompts, respectively, and press 'Return' on the keyboard.
   Define whether alignment gaps and ambiguities within individual marked sequences (species) should be taken into account:
   Use the right mouse button to display the submenus associated to the items below the 'markerline:' prompt by pressing the respective buttons.

       don't count:
               Calculate conservation from unambiguous
               bases only

       don't use column if maximal:
               Exclude column if the respective symbol
               is present in the majority of the marked
               sequences.

       exclude column:
               Exclude column if the respective symbol
               is present in any of the marked
               sequences.

       treat as ambiguous:
               Take the respective symbol as an
               unambiguous residue.

2. After selecting columns define how to treat ambiguities for distance calculations:
   Use the right mouse button to display the submenus associated to the items below the 'distance matrix:' prompt by pressing the respective buttons.

       don't count:
               The particular position is not
               included for binary distance
               calculations if the symbol is
               present in one or both sequences.

       use distance table:
               the symbols are treated as unambiguous
               residues

3. Calculate profiles and matrices:
   Use the right mouse button to display the 'CALCULATE' menu and select 'markerline' (profile) or 'distance matrix' by releasing the mouse button while the cursor is positioned on the respective menu button.
4. Display results:
   Use the right mouse button to display the 'VIEW' menu and select 'species', 'markerline' or 'distance matrix' by releasing the mouse button while the cursor is positioned on the respective menu button. The names, the aligment of the marked sequences and the conservation profile, or the distance matrix are shown within the display area, respectively.
   The profile:
   The fraction of sequences sharing most frequent residue at a particular alignment position is shown as a number to read bottom down. Alternatively, the profile can be displayed as a curve by pressing the <toggle> button in the left part of the window. It can be smoothed by selecting a number from the 'smooth' menu (left part of the window).
   Editing the aligned sequences and profiles, a name can be selected by moving the cursor to it and pressing the left mouse button. Pressing the <reference> button, the respective sequence is used as a filter superimposed to profile. This allows to exclude further positions from subsequent calculations which are not occupied by bases in the reference.
   Tha matrix:
   Editing the matrix, mean values can be calculated for groups of organisms displayed as triangles (radial tree) or rectangles (dendrogram) in a tree stored in the database. The grouping currently or most recently displayed is used for selecting sequences for the calculation of mean values. Select a tree by pressing the <grouping> button in the left area of the window.
5. Save results:
   To export distances and profiles (not graphs!!) to ascii files, use the right mouse button to display the 'SAVE' menu and select the corresponding menu item by releasing the mouse button while the cursor is positioned on it.

       uncoded mline:
               The positional conservation is encoded
               by a sequence of letters: A = 1%,
               B = 5%, ...., Z = 100%.

       bin mline:
               Included and excluded columns are
               indicated by 1 and 0, respectively.

       % dif. matrix:
               Dissimilarity values.

       % sim. matrix:
               Similarity values.

       phyl/prot distmat:
               Corrected distances according Jukes and
               Cantor (nucleic acid sequences only).

       pos. vari:
               Number of different residues at the
               particular alignment position.

6. Reconstruct a tree:
   Press the <NEIGHBOR> button. The tree is reconstructed using the neighbour joining method and is stored in the database as 'tree_neighbour'.
7. Store profile in the database:
   Press the <ARBSAVE> button to store any calculated profile 0 / 1 encoded in the database (SAI). The profile can be used as filter for other ARB tools.

## NOTES

### A new version of the tool is under development.

### It is recommended to calculate profiles here, to save them in the database, and to reconstruct distance matrix trees using 'ARB_NT/Tree/Neighbour joining' in combination with the profile as filter.

## EXAMPLES

### None

## WARNINGS

### Whenever text is typed to the window, press 'Return' on the keyboard, to ensure that the information is recognized by the program!!!

## BUGS

### No bugs known