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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

Database Query - TREES

tree

The Trees TAB allows you to view a tree of the isolates returned from your initial query, using either allelic profiles differences or concatenated allele sequences, or a tree of these isolates compared with those from a second query.

On clicking the 'Trees' TAB you will be presented with a link to view a Neighbor-joining tree based of the isolates returned from your initial query, using either allelic profiles (the default) or concatenated allele sequences.

Below this is the option to fill in a second query form, to use a tree to compare the isolates from your initial query wit those from the second query.

The screenshot below will compare the isolates from the initial query on the S. pneumoniae database (serotype 9V isolates) with the those from a second query for isolates of serotype 14.

 

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When you have entered your comparison query clicking 'submit' will take you to the tree viewing page, as in the following screenshot:

 

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As with eBURST, colours are utilised to indicate STs from your initial and comparison queriesand your initial query.

 

Is this the best tree style to show?? Lots of pink so actually showing STs and not isolates???

 

STs will be coloured BLACK if all isolates of the ST are serotype 9V (the initial query)


STs will be coloured PINK if the ST includes both serotype 9V and serotype 14 isolates


STs will be coloured GREEN if all isolates of the ST are serotype 14 (the comparison query)

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). The '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. ST labels can be shown or hidden (as in the above tree).

You can save the image as a PNG file by clicking 'Save as PNG' WHERE???

FULL SCREEN - change tree method - NJ or UPGMA.

 

In the next section we describe downloading the results of your query.

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