Roci - Manual

• Input
• Options
• Output

Input

To keep the in- and output files clearly arranged, the structure of the phylogenetic tree and its annotation are seperated into two blocks. One block describes the structure of the tree and the second one annotates the leaves.

Before the first block begins, the file content is arbitrary. You can use this to comment your data.

The first block is indicated by a line, which only consists of the keyword tree:. The following lines contain the structure of the phylogenetic tree in a form simular to the Newick tree format [phy]. This format enables a simple, flat ascii-representation of a tree.

• Leaves are represented by their names.
• Interior nodes are represented by a pair of matched parentheses. Between them are representations of the nodes that are immediately descended from that node, separated by commas.
• Interior nodes can have names. These names follow the right parenthesis for that interior node.
• A name can be any string of printable characters except blanks, colons, semicolons, parentheses, and square brackets. It can also be empty. An unnamed node will be named automatically.
• The tree ends with a semicolon.
• You can put whitespaces, tabs or newlines nearly everywhere in the tree.

The second block has to start with a line, consisting of mapping:. After that, you have two possibilities to annotate each leaf node:

• A leaf can be annotated by a gene order, by writing the name of the leaf and the gene order, separated by blanks, tabs or newlines.
  The gen order has to be composed of all numbers from 0 up to an arbitrary n, each of them unsigned or signed by a minus symbol, seperated by blanks and enclosed by < ... >. It is not allowed to skip a number or to use it twice.
• Alternatively, a leaf can be annotated by a set of conserved intervals. In this case, a PQ-Tree is used to represent a saturated set or permutations.
  The format of a PQ-Tree is simular to the tree format described above: Use all numbers from 0 up to an arbitrary n, each of them unsigned or signed by a minus symbol, as names for the leaf nodes. It is not allowed to skip a number or to use it twice. It is not allowed to skip a number or to use it twice. Iinterior nodes can not be named. Q-nodes are represented by square brackets and P-nodes by round parentheses.

Example:

tree:

((Leaf_1, Leaf_2)Node_1,
(Leaf_3,Leaf_4))Root;

mapping:

Leaf_1 < 0 1 2 3 4 5 >
Leaf_2 < 0 -3 -2 1 4 5 >
Leaf_3 [0,1,(2,3),4,5];
Leaf_4 [0,(-2,[-1,4,3]),5];

Output

The output consists of three parts:

• The input,
• the result of the bottom-up phase and
• the result of the top-down refinement.

Each part is composed of a tree-block and a mapping-block as described for the input.

Options

• Verbose mode: During both phases of the Labelling-Algorithm, all intermediate results for each labelled or refined node are shown: Conflicting singletons, conflicting subsets, neutral intervals etc.
• Extended search space: This option allows to search through all conserved intervals while looking for conflicting subsets. The default mode is to search through the irreducible conserved intervals only.