Species tree editor

This editor is able to visualise important species trees (tested with more than 10,000 leaves) in order to modify them. It is possible to choose branch lengths, or to reduce some nodes.


The menu bar

It provides another way to use the tools of tool bar, describe later. It also permits to save, save as and load species trees with the format described here. It is possible to import species trees from a more classical format: text files with tabulated trees, species, synonyms and without branch lengths. These trees can be found at: http://www.ncbi.nlm.nih.gov/Taxonomy/

For example:

20# RAJIFORMES ==> 160 seqs.

Synonym: BATIDOIDIMORPHA

{[order] rays}

21# RAJIDAE ==> 160 seqs.

{[family] skates}

22# RAJINAE ==> 160 seqs.

{[subfamily]}

23# RAJA ==> 160 seqs.

{[genus]}

24# RAJA ERINACEA ==> 123 seqs.

Synonym: RAJA ERINACIA

{mtgc:2|[species] little skate}

24# RAJA MONTAGUI ==> 3 seqs.

Text between {} are comments. Synonyms are taken into account.

The option "close" close the editor, and the option "apply and close" choose the last saved version of the current tree as global species tree, before closing.


Tree window

This window is used to see, travel in and modify the species tree. A right click in the panel centres the vision at mouse position. To complex families for current zoom are hidden by a grey triangle (green nodes).

 Bring the navigator to the front of the window.

 Refresh editor window to initial vision.

 

There are two tool categories.

Visualisation tools:

 Zoom in, keeping the vision centre constant.

 Zoom out, keeping the vision centre constant.

 Hide/Show pointed node.

 Force the vision to a pointed part of the tree.

 Go back to the current root father.

 Go back to global tree.

 

Modification tools:

 Unlock locked node (see next tool).

 Check the depth of the pointed family, and lock it. Refresh every tree branch lengths to keep the initial proportions. Keep other locked family unchanged. This tool guarantee the tree ultrametry.

 Check the pointed locale branch length. Nothing guaranteed.

 Reduce pointed node: the node is deleted and its sons are brought back to its father.

 Delete the pointed node and its subtree, and replace it by a leaf with species name equals to the concerned family.

 Check the total depth of the tree, keeping the initial proportions.

 Add to leaves a branch length, in order to let them have the same total depth.

 Undo the last use of any modification tool.

 


Navigator

 

This tool make easier travels in species trees. The first line (in grey) is the current node name. The list is those of the current node sons. The distances between the current node and its sons are annotated to the left.

 Back to current node father.

 Forward to highlighted son.

 Centre vision on current node.

 Set current node to pointed node.


If you have problems or comments...

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