This window is the principal interface used to reconcile phylogenetic trees. It permits to load the global species tree or launch its editor. You may also load, root or reconcile gene trees, and check the constants ruling the reconciliation. An information box describes the historic of every operation made earlier.
The menu bar
It provides another way to use the tools of the internal windows, describe later. It also permits to quit the software in menu "File". The menu "default" is useful to choose current path as default path, in order to load species and gene trees. The button "refresh" reorganise the different internal windows in the desk.
Species tree chooser
It is the window which permits to manage the species taxonomy and their colour representation.
It launches the species tree editor which permits to modify and import species trees.
The button used to choose the global species tree. It accepts text files (easily with the extension ".spt") containing a species tree in the newick format. For example:
((MUS:10.5,RATTUS RATTUS:10.5)RODENTIA:20.0,(HOMO SAPIENS:16.0,MACACA:16.0)PRIMATES:15.5)MAMMALIA:10.0;
The tree is only in the file first line and contains branch lengths (from a node to its father).
It permits to switch between an automatic colour mode and a configurable colour mode. Automatic mode chooses arbitrarily a colour for each species (recommended). The configurable mode reads the colour conventions in the file "color.cfg". It contains several levels of colours with at most twelve species of species group (configured with demonstration data).
Gene tree chooser
From this point, you can load, root, reconcile and save gene trees. You can numerate orthologous gene families and save results in a text file.
Select every tree of the list.
Unselect every tree of the list.
Add gene tree file(s). They consists in text files containing each gene with the corresponding species, and a newick gene tree with branch lengths and eventually a "bootstrap" value. These trees can be found at: http://pbil.univ-lyon1.fr/databases/hovergen.html For example:
OAAIII.PE1 Ovis aries
CHKSPINH.PE1 Gallus gallus
HUMATH3U7.AT3 Homo sapiens
HUMATH3A2.AT3 Homo sapiens
S47225.PE1 Mus sp.
S79838 Gallus gallus
AF006495.PE1 Cyprinus carpio
AB027238.PE1 Cavia porcellus
AB026832.PE1 Takifugu rubripes
ASA252153.PE1 Salmo salar
Remove from the list any selected gene tree file.
Save in the same files selected gene trees with current root and reconciliation.
Save in another file the first selected gene tree with current root and reconciliation.
Save in a text file orthologous gene families issued from every selected file. For example:
FAM001.gnt 1 AF006495.PE1
FAM001.gnt 1 AB026832.PE1
FAM001.gnt 1 ASA252153.PE1
FAM001.gnt 1 HUMATH3A2.AT3
FAM001.gnt 1 HUMATH3U7.AT3
FAM001.gnt 1 AB027238.PE1
FAM001.gnt 1 S47225.PE1
FAM001.gnt 1 OAAIII.PE1
FAM001.gnt 1.1 CHKSPINH.PE1
FAM001.gnt 1.2 S79838
Reconcile every selected and rooted gene tree. An exhaustive species tree must be loaded.
Reconcile and choose a root for every selected gene tree. An exhaustive species tree must be loaded.
Open the results window of the corresponding tree.
It permits to choose parameter values which rule the reconciliation and the root choice.
Maximum bootstrap for reduction: A branch will not be reduced during the reconciliation if its bootstrap is greater than this value.
Maximum length for reduction: If the gene tree is not bootstrapped, the branch value is evaluated with its length. A branch cannot be reduced if its length is greater than this value.
Maximum length for reduction: The branch value in a species tree is evaluated by its length. The branch cannot be reduced if its length is greater than this value.
Maximum relative rate ratio before duplication: Supposing that the mutation rate is constant between genes, the branch lengths in a gene tree can be estimated comparing them by those in the species tree. If a branch is X times too short, X equals to the maximum relative rate ratio, the considered node will be interpreted as a duplication.
Maximum length for polymorphism: A gene tree with a length from node to leaves lesser than this value will not be reconciled, and concerned genes be interpreted as an orthologous gene family.
Maximum depth for best root research: The root is chosen by minimising the number of duplications. The research is made to this maximum depth, from the starting point.
Apply the values contained in the text boxes to next reconciliation.
Save current parameters as default parameters.
Reload default parameters.
Permits to access to more precise informations about parameters directly in the software.
This window contains historic of every operation, successful or not.
Clear the information box.
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