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Instructions

Introduction

MLST-Maps
    eBURST
    Trees

Database Query
    Results
    Maps

    eBURST
    Trees
    Download Data

Locus Query
    Sinlgle

    Multiple
    Batch

ST & Profile Query
    Sinlgle
    Batch
    ST Query

eBURST
    User data
    Geographic

Downloading Data

Organism Specific

Submitting Data
    alleles
    Sequence Types
    Isolate data
    Next-gen data

 

Policy Document

MLST-Maps - Trees

tree

The Trees TAB allows you to compare isolates from a selected country with those from another country(ies), using different terminal node colours to indicate on the tree their geographic source. These comparative geographic trees can be drawn using differences in allelic profiles or concatenated allele sequences.

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.

8

 

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


STs found both in your initial country and the comparison country(ies) are coloured PINK


STs found only in your comparison country(ies) are coloured GREEN

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.

 

 

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