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];
