output - sungsik-kong/PhyNEST.jl GitHub Wiki

Visualization and output interpretation

Once the analysis is complete, PhyNEST creates two output files with extensions .log and .out. By default, these files are named as either PhyNEST_hc or PhyNEST_sa, depending on whether the hill climbing or simulated annealing strategies were used, respectively. Note the output file name can be changed to a user-desired name using the optional argument filename="" when running phyne!(args). The .log file contains the output printed on screen throughout the analysis.

The .out file contains two (extended) Newick strings on lines 1 and 3 (see below).

The two strings represent the same topology, but the one on top is formatted for PhyNEST, PhyloNetworks, and PhyloPlots and the bottom is formatted for DendroScope. Simply, the extended Newick for DendroScope does not contain information on inheritance probabilities assigned to the hybrid node because it cannot read them. We provide both version to maximize interoperability. See here for detailed explanation on how to visualize a network using PhyloPlots.

To visualize the network using DendroScope, open DendroScope and browse to File>Enter Trees or Networks.

Copy and paste the bottom Newick in the .out file into the to prompt, then click OK. Check Edge lengths if the extended Newick string contains branch lengths.

Voilà!