Modeltest is an advanced and reliable piece of software developed to serve genetics engineers in determining the differences between DNA substitution models using hierarchical hypothesis testing in order to generate the results.
Command line interface
The application is fairly complex, as it is meant for experienced users with a solid background knowledge in genetics as well as computers, specifically since it does not provide users with a GUI, running only through the command line interface, which can make it fairly challenging for novices.
Nonetheless, Modeltest does not require installation, so it suffices for users to just drop the executable file onto an open instance of Command Prompt and press the Enter key, which in turn will reveal the program's functions along with a brief explanation of the available commands.
Functions and running parameters
Modeltest is meant to work with files generated by PAUP* which contain the genetics information required, as well as files which comprise raw log scores along with parameter estimates for the assessed models.
On the opposite end, the utility generates a description of the probability ratio tests that were conducted, and their corresponding P-values, information which is then interpreted and assigned a proper model.
The supported models are listed in the command line interface, including JC (Jukes and Cantor), TrNef (Tamura-Nei with equal base frequencies), TIM (Transitional Model), GTR (General Time Reversible), F81 (Felsenstein) and several more.
At the same time, users can work with a specific set of functions, exemplified in the main window in order to make them easier to understand and employ. As such, users can determine the debug level ( -d), the alpha level (-a), the number of taxa (-t), activate the LRT calculator mode (-l), determine confidence interval for averaging (-w) or use BIC rather than AIC for all future operations (-b).
A comprehensive instrument for determining the proper substitution model
To conclude, Modeltest is an efficient application developed for professionals working in the field of genetics, offering them the means of comparing DNA substitution models, thus helping users decide on which best fits their data.

To download and install Freeware with direct links, choose Freeware or Here We Go (…), next right, Save File location, then Choose Save file location.

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Modeltest Usage:

At first, if you are new to the program, follow the instructions on the Modeltest website, they will explain everything to you and how to run the program.

If you are interested in using modeltest to compare DNA substitution models, check its information on the website:

Modeltest Extends:

This model was used to calculate the best model for the Cytochrome oxidase I gene sequences for Cicindela monticola from Anhui, China.

Modeltest History:

This program is part of the public domain (see this page for license).
It was last modified on 25-Aug-2006.
For more information about the Program you can visit the program’s home page.Non-Native Species

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Model-Testing Environment
The program was developed for geneticists working in the field of molecular genetics, offering them the ability to determine the model that best fits their DNA sequences.
Modeltest Model Types
Modeltest supports a variety of model types, including:
JC (Jukes and Cantor)
TIM (Transitional Model)
TrNef (Tamura-Nei with equal base frequencies)
GTR (General Time Reversible)
F81 (Felsenstein)
In addition to that, Modeltest is capable of calculating the probability ratios for all models according to the new method of Maddison and Tavaré (1987), known as the “log-parity method”, therefore making it compatible with PAUP*, the genetic algorithm designed to determine those ratios.
How Modeltest Works
When the user places a raw log score (when available) or a file with the sequencing information on the command line, Modeltest will automatically generate the log scores which can be inputted, thus allowing the user to bypass PAUP* entirely and provide them with the model that best fits their data.
Users have the ability to determine the model that best fits their data from their own original log scores using Modeltest’s API (Application Program Interface), and since the main purpose of the program is to compare substitution models, having the ability to calculate and determine the probability ratios required in the determination of the model is a huge advantage.
Modeltest Models
Modeltest supports a variety of model types including:
JC (Jukes and Cantor)
TIM (Transitional Model)
TrNef (Tamura-Nei with equal base frequencies)
GTR (General Time Reversible)
F81 (Felsenstein)
Modeltest Features
A critical and unique feature of Modeltest is that it calculates and tests the parameters of the models, yielding the probability ratios for all of them in the process.
Modeltest’s interface is user friendly and offers the user a set of functions and parameters in the main window. The user is allowed to define a maximum number of taxa to be tested by the software, which in turn generates log scores for up to these maximum taxa.
Moreover, the user is also given a choice of whether they want to perform single, multiple, partitioned and selfing evaluations, which are all necessary for determining the model that best fits their data.
A simple explanation of each of these tests may be seen

ModelTest is a relatively new modeler. It has the ability to run all the available transition/transversion, substitution matrix, hemi-sharp, substitutional equilibrium (‘gap’), and equilibrium frequencies models (and even a few models that I haven’t tried) and to detect tree size effects.
But ModelTest has a little problem for me… It generates the same tree topology for every transition/transversion, substitution matrix, hemi-sharp, substitutional equilibrium (‘gap’), and equilibrium frequencies models that I run. This makes it very easy to get the same tree, even though I use different model parameters.
I took a walk around the authors website and found that they have a ‘Model selection guide’ on how to choose a good model. This should help greatly!
I do not know whether ModelTest will run all models that are available in PAUP or whether it will just run the default ones that are placed in the tree folder.
Best of luck!

Phylip is a common package for handling phylogenetic data and tree construction algorithms, supporting various input formats. A tool known as Consel is often used in conjunction with Phylip to display, modify and visualize input sequences and trees.
This article describes the commands available through Consel, which can be used as a tool for sequence comparison and tree visualization.
Sequence alignment and display
Running Consel from the Phylip directory will display a window where users can enter, add and delete sequences. To do this, users need to paste or type the sequence into the first window, followed by a tab and enter. Then the sequence must be selected within the second window using the mouse. The third and fourth windows allow users to edit a sequence by removing tags, changing the sequence name, and identifying insertions and deletions.
To keep a record of the pasted sequences, Consel supports its own file format named something like tss. Each sequence is stored with a tag, followed by the sequence name, and a sequence number. The sequence name can be edited in the fifth window, as can the sequence number. The tss format can store multiple sequences in a single file, allowing users to easily manage different sequences. When the sequences are finished, users press the Save button, allowing Consel to save the modified file.
Phylip currently supports five input file formats for inputting sequences: Phylip, PHYLIP, DOS, Newick and Fasta. Fasta is a standard format used by many

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