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Non-Negative Additive Arithmetic (NONA) is a command-line software system for constructing phylogenetic trees using parsimony methods.

It’s entirely composed of ANSI C and Free Software Technology for reliable development.
It runs very fast and efficiently on most modern Linux systems, and can be installed and launched by using just its own installer.
It needs a Text-based UIs like GNU Emacs, vim, or nano to be utilized; however, it has its own text-based CLI, which can still be utilized if the mentioned software isn’t available and/or accessible.
Installation Process:

Download the current available version of the app’s installer.
Move this file into your application’s folder, which is represented by the “Program files” folder within your computer. (in other words, the location of your computer’s default file manager).
Open Command Line Service within your Operating System’s Run window, and navigate to the folder where you have moved the file.
Click on the file to begin installation.
The software will perform its installation and launch automatically.

After the initial installation, you can quit from the program and then run it using the command./nona or the solution’s shortcut, which will be located in your Desktop.
This particular app can be run on both 32- and 64-bits Linux systems, Windows, Mac OS X, and many other Operating Systems.

NONA CLI:

You can get all the required options for Non-Negative Additive Arithmetic (NONA) through the usage of its CLI.
Unlike the main GUI, this user-friendly interface lets you work with the program using parameters in order to navigate the entire list of options available.

For instance, if you’d like to open up the parsimony option, you should enter./nona -p

You can download the complete archive of NONA’s CLI to your system, so you’ll be able to get the same options in a very simple fashion.

This utility is very helpful for further learning, debugging, and some other purposes.

Non-Negative Additive Arithmetic (NONA) Versions:

NONA is in its second beta stage, which is not perfect, since there are still some bugs and the code isn’t exactly finished yet.
It’s free and open-source, so if you are interested in learning more about the project, you can visit the NONA

NONA Free

NONA is a software solution that helps phylogenetic and evolutionary biologists perform phylogenetic analyses automatically. The program’s users can utilize NONA without any prior training in computational phylogenetics or evolutionary biology.
The programs come with pre-compiled parsimony analysis programs, and an option of using MINIQ analysis software for phylogenetic tree reconstruction.
It supports various file formats for phylogenetic analyses such as Newick, Nexus and Phylip. Researchers can run phylogenetic analysis through non-parametric bootstrap analysis, jackknife analysis, as well as parameter estimation analysis. The result of each analysis can be saved in a tree format for further processing.
It supports the following molecular data types: DNA, RNA, and Protein. Additionally, it offers a program to generate maximum likelihood trees.

What’s New in Version 2.5:

Added support for EAZY analysis programs.
Added program options to change species input tree input.
Bug fixes.

Software Licensing:
NONA is a Shareware application and can be downloaded for free. After the download completes and launches, you will be presented with a dialogue that asks you to accept the licensing agreement.

NONA Uninstaller:

NONA Uninstaller is a tool that was designed to enable you to easily remove NONA from your system and completely erase its traces, including the app’s registry entries and files.
The tool provides you with an option to select all NONA installations, so you can remove the software and its related components from your system at once.
First, launch the tool and click Next.
Afterwards, select the component of NONA you want to remove, then click Next.
Then, select the folder where the NONA uninstaller was installed, and click Next.
Click Finish to complete NONA uninstall.

NONA Full Uninstaller:

NONA Full Uninstaller allows you to completely uninstall NONA using an intuitive graphical interface.
In the main window, click Add, then click Install to select NONA and click Next.
Click Edit to add more applications that you want to remove, then click Install to complete NONA uninstall.
The application allows you to select the installation folder you want to remove the software from.
You can also choose the uninstallation method you want to use (complete uninstall, remove the application’s registry entries, uninstall the supporting files, etc.).
In order to find more information regarding NON
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Supported File Formats:
The application accepts just about any kind of tree file, which can be actually built using one of two types of parsimony software: PAUP\* \[[@B1-genes-11-00733]\] and TNT \[[@B2-genes-11-00733]\]. This application also allows you to perform online searches for the desired data, thus generating it if needed.
Command Line Arguments
Each argument can be accompanied by a multiple of operations, thus allowing you to perform a series of operations on the tree at once, if needed.
An example would be to perform the following tasks:
- - Find the shortest tree for the given data
- - Calculate the sum of consistency index (CI)
- - Calculate the sum of retention index (RI)
- - Calculate the sum of tree length (TL)
- - Calculate the sum of optimal tree length (TL~opt~)
- - Calculate the sum of the bootstrap frequencies (BSF)
 - - Calculate the overall mean of the bootstrap frequencies (BMF)
- - Calculate the overall mean of the a posteriori frequencies (APMF)
- - Calculate the average of the bootstrap frequencies (BS~avg~)
- - Calculate the average of the posteriori frequencies (AP~avg~)
- - Generate a consense tree
- - Generate the optimal tree
- - Generate the most parsimonious tree
- - Generate 50 shortest trees
- - Generate 1000 shortest trees
- - Generate the lowest tree cost tree
- - Calculate the lowest tree cost
- - Calculate the most parsimonious tree
- - Generate a consensus tree
- - Generate a tree with the largest overall mean of the bootstrap frequencies
- - Generate a tree with the smallest overall mean of the bootstrap frequencies
- - 

What’s New in the NONA?

=====================================
Non-Node-Aligned
The most useful of the Parsimony Programs, and the most versatile of all…
The non-node-aligned Parsimony Programs you will find here are simpler to use than those that require a phylogeny tree diagram. They are also slightly slower, but perhaps with a little practice they can be made to be as fast as the other parsimony programs as well.
=====================================
Non-Node Aligned
Non-Node Aligned Parsimony Programs
=====================================
Visual Non-Node Aligned Parsimony Programs
=====================================
Use the visual non-node-aligned parsimony programs to display separate character states for characters that are not known to occur in a focal clade of interest. The programs use an input tree as their starting point, and add missing character states and reduce character changes as a cost optimization problem.
=====================================
Visual Node-Aligned Parsimony Programs
=====================================
Use the visual node-aligned parsimony programs to display separate character states for branches of a focal clade of interest. The programs use an input tree as their starting point, and add missing character states and reduce character changes as a cost optimization problem.
=====================================
Node-Aligned
Node-Aligned Parsimony Programs
=====================================
Non-Node-Aligned Parsimony Programs
=====================================
The non-node-aligned parsimony programs are simpler to use than those that require a phylogeny tree. They are also slightly slower, but perhaps with a little practice they can be made to be as fast as the other parsimony programs as well.
=====================================
Non-Node Aligned Parsimony Programs
Non-Node Aligned Parsimony Programs
=====================================
Visual Non-Node Aligned Parsimony Programs
=====================================
Visual Non-Node Aligned Parsimony Programs
=====================================
Visual Node-Aligned Parsimony Programs
=====================================
Visual Node-Aligned Parsimony Programs
=====================================
Node-Aligned Parsimony Programs
=====================================
Node Aligned Parsimony Programs
=====================================
Node-Aligned Parsimony Programs for Parsimony Networks
=====================================

NONA might not look like much at first glance, but it’s packed full of useful functionality!
NONA can be used to:
—————————————————-
– construct parsimony-informative phylogenies
– calculate consensus trees from parsimony-informative

System Requirements For NONA:

One or more players. On play, the number of players should be set to the number of consoles being used.
Internet connection required.
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