What does scale bar mean in phylogenetic tree?

The scale bar can be used to define the scale of branch lengths if they display some kind of node data in the phylogram/chronogram-view. Although it is also possible to have a scale bar in the rectangular cladogram-view it will usually not make any sense.

What is the neighbor-joining method?

The Neighbor-Joining Method. The neighbor-joining method is a special case of the star decomposition method. In contrast to cluster analysis neighbor-joining keeps track of nodes on a tree rather than taxa or clusters of taxa. The raw data are provided as a distance matrix and the initial tree is a star tree.

What does the scale on the bottom of the tree indicate?

The longer the branch in the horizonal dimension, the larger the amount of change. The bar at the bottom of the figure provides a scale for this. In this case the line segment with the number ‘0.07’ shows the length of branch that represents an amount genetic change of 0.07.

How is neighbor joining used to optimize trees?

Nonetheless it is important to note that, given an additive distance matrix as input, neighbor joining is guaranteed to find the tree whose distances between taxa agree with it. Neighbor joining may be viewed as a greedy algorithm for optimizing a tree according to the ‘balanced minimum evolution’ (BME) criterion.

What do you need to know about neighbor joining?

Usually used for trees based on DNA or protein sequence data, the algorithm requires knowledge of the distance between each pair of taxa (e.g., species or sequences) to form the tree. Starting with a star tree (A), the Q matrix is calculated and used to choose a pair of nodes for joining, in this case f and g.

What do the two iterations of neighbor joining do?

Two more iterations lead first to (D), and then to (E), at which point the algorithm is done, as the tree is fully resolved. Neighbor joining takes as input a distance matrix specifying the distance between each pair of taxa.

How is neighbor joining used in minimum evolution?

Neighbor joining as minimum evolution. Neighbor joining may be viewed as a greedy algorithm for optimizing a tree according to the ‘balanced minimum evolution’ (BME) criterion. For each topology, BME defines the tree length (sum of branch lengths) to be a particular weighted sum of the distances in the distance matrix,…