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PAINT is a Java application for viewing and annotating phylogenetic trees.
- The program is still a bit bug-y, but the developers are more than willing to listen and make changes.
- Download from sourcefouge of Panther -- http://sourceforge.net/projects/pantherdb/files/PAINT/
- Open terminal, go into folder & type ./launchPAINT.sh
- PAINT will do a bunch of stuff & open a GUI
- Go to “File” & click on “Log in” – it will do this automatically (b/c it’s a local install)
- Go to “File” & click on “Open from database”
- Pick a gene to search for – mutL & click on “Search”. Wait.
- Once it builds the tree, you can look at what has exptal evidence (red gene names) & what doesn’t (grey gene names).
- You can drag & drop annotations (i.e. DNA binding, ATP binding) to various branches of the tree when you get a green + symbol (ok by taxon constraints)
- - When you try to drag & drop an inherited annotation onto a wacky branch, i.e. something that fails taxon constraints, it will not let you drop the annotation.
- - i.e. if you try to drop a pollen process term on non-plants, it won’t even offer you the green +
- - When you drag & drop, the red gene names (with exptal evid) stay red, but the grey genes under that node now show in blue & have an annotation with the evidence code of IBA (inferred by biological ancestor).
- If you close the window, you will have to re-launch the program from the terminal!!!
- - I have NOT figured out how to “undo” - Suzi says "undo" is broken!
- At the bottom is a list of Annotations & Evidence – annotations are obviously those with exptal evidence, evidence is for you to put in text – how to think of the annotation spread, why you made that spread, why this is wrong or that is wrong. IS visible to the public – when make the GAF???
- - Similar to our notes field from CACAO (what fig, table)
- In the trees constructed for any gene, there are circles & squares -- circles are speciation events, squares are duplications.
- - If you right click on one of those symbols, you will be able to "collapse node" (still in tree, will get propagated annotatinos) , reroot to node (we only want to look at this node and not other stuff) , output seq ids for leaves, Prune (get rid of this entirely from the tree, does not get propagated annotations).
- - When you collapse a node, it will be a rectangle instead. If you scroll over in the "Protein Information" tab, it will tell you what species/family/etc.
- When you want to, go to "File" and "Save annotations". This will make a series of files, including a GAF file on your desktop. You can then use this file as something to open instead of the "Open from database".
- what PAINT still cannot do is judge how “evolve-able” the sequences are.
- useful form of QC b/c should paint a coherent picture – gives context for annotators
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