# 3.2. NetME¶

NetME constructs a minimum evolution (ME) tree from the specified split network with an implied circular order. Such split systems can, for example, be generated by the NeighborNet algorithm or any for constructing phylogenetic networks (see Netmake). More specifically, NetME is the implementation of an O(n 4 ) algorithm for finding an optimal minimum evolution tree in a circular set of splits where the set of species is of size n. For more information on the algorithm please see and please cite (S. Bastkowski et al, 2014).

NetME takes in a nexus file containing a distance matrix and a circular split system (such a file can be generated by running Neighbor-Net via netmake). NetME produces two output files:

- The weighted split system, in nexus format, corresponding to a restricted minimum evolution tree, where the weights are recalculated by using a Non-Negative Least Squares (NNLS) method.
- A file containing the tree length of tree weighted with Ordinary Least Squares (OLS).

In addition the user can request to output, using the ‘-l’ option, the weighted split system, in nexus format, corresponding to a restricted minimum evolution tree, where the weights are derived from the Ordinary Least Squares (OLS) method used for constructing the tree.

NetME can be run from the command line like this:

```
netme [-o <output_prefix> -l] <nexus_file>
```

Alternatively, NetME can be invoked through the Tools menu in the SPECTRE graphical interface.

## 3.2.1. References¶

- Bastkowski, A. Spillner, V. Moulton (2014) Fishing for Trees with NeighborNets. Information Processing Letters 114(1-2): 13-18.