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TITLE		Matrices, Masks, Profiles V1.0

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
