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# Branch analysis

## DESCRIPTION

### Functions provided here may be useful to

• detect wrong placed species or groups (or poor data, which might also lead to wrong placement)
• detect anomalies caused by (wrong) tree reconstruction
• gather information about tree topologies.

## Analyse distances in tree

### For the whole tree

• the in-tree-distance (ITD = sum of all branchlengths) and
• the per-species-distance (PSD = ITD / number of species) are displayed.

### For all leafs in the tree the following values are calculated:

• mean distance to all other leafs
• minimum distance to any other leaf
• maximum distance to any other leaf

## Using the PSD to compare trees

### The PSD is useful when comparing tree topologies (based on similar sets of species) that were reconstructed using different methods. Imagine you have two trees:

• tree_raxml (reconstructed with RAxML)
• tree_arbpars (reconstructed with ARB parsimony)

### The PSDs of both trees will be quite different (maybe by factor 50 or 60). Calculating the ratio of both PSDs, give you a good value for scaling the branchlengths of (a copy of) one of the trees. For example the PSDs might be

• PSDr = PSD(tree_raxml) = 0.002219
• PSDp = PSD(tree_arbpars) = 0.118483

## Mark long branches

### 'Distance' here is the sum of all branches between the furcation and the least distant leaf of the left resp. right subtree.

```Relative difference     Meaning
The nearer subtree has at least
10%                     90%
50%                     50%
75%                     25%
90%                     10%
of the farther subtrees distance.```

### The indented workflow is

• search long branches
• check alignment and data and fix any problems
• recalculate tree parts (see ´Add species with local optimization´)
• search again. Now you may find other branches, nearer to the tree root.

## Mark deep leafs

### Marks alls leafs in tree that have

• depth above min.depth and
• root-distance above min.root-distance

## Mark degenerated branches

### Common reasons for degenerated trees:

• subsequently adding species using the 'quick add marked'-feature of ARB parsimony without ever optimizing the whole tree.
• some "phylogenetic areas" are explored more thoroughly than others, resulting in unbalanced representation of the evolution as it took place. This is especially relevant if your database contains many clone-variants and you try to calculate a tree.
Solutions:
• Optimize your tree. For big trees you might try to
• mark questionable species using this function and then
• perform local/global optimization of marked species in ARB parsimony.

• Replace over-represented areas by one or few representatives (see also ´Cluster detection´). Calculate a new or optimize an existing tree with that subset of species. Then quick-add previously removed species into that tree.