MLST-Maps - Trees
On clicking the 'Trees' TAB, you are presented with a list of continents (which can be expanded to view a list of countries within each continent) from where isolate data have been deposited in the MLST database. Each country where isolate data are available has the number of isolates indicated in parentheses.
For example, the following screenshot compares isolates from Australia and New Zealand with those from the initially selected country - Brazil. The default tree building option is chosen - using differences in allelic profiles.
After selecting your comparison countries (Australia and New Zealand), clicking 'submit' brings you to the tree viewing page, as in the following screenshot
As with comparative eBURST, colours are utilised to indicate the isolates from the different countries, as follows:
How does this colouring work - if you show STs on a tree the following is correct buit if you show each isolate surely you will just see black nodes or green nodes - you cannot have an ISOLATE from both countries, only a ST???
Is this the best tree style to show??
STs found only in your initial country are coloured BLACK
You can click and drag to move the tree and to the right of the tree are controls that allow you to change the tree type (radial, rectangular or circular). 'Sliders' allow you to zoom into the tree, change the size of the circles representing the terminal nodes and to change the size of the text used for ST labels.
You can save the image as a PNG file by clicking 'Save as PNG' - ???? where - how??? this only seems to work if redraw as fullscreen - need to say right click and save as.
FULL SCREEN - change tree method - NJ or UPGMA, click internal nodes to fire off map for multiple STs - say what type of tree it is ..
In the next section the Database Query section of the site is described.