ProtTest Crack

PROTTEST (ModelTest’s relative) is a program for selecting the model of protein evolution that best fits a given set of sequences (alignment). Models included are empirical substitution matrices (such as WAG, LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam, MtArt, HIVb, and HIVw) that indicate relative rates of amino acid replacement, and specific improvements (+I:invariable sites, +G: rate heterogeneity among sites, +F: observed amino acid frequencies) to account for the evolutionary constraints impossed by conservation of protein structure and function. ProtTest uses the Akaike Information Criterion (AIC) and other statistics (AICc and BIC) to find which of the candidate models best fits the data at hand. Give ProtTest a try to fully assess its capabilities!

 

 

 

 

 

 

ProtTest Incl Product Key

License: free to download and use.

See Also:
– (2016) An improved statistical method for model selection in phylogenetics

Open Issues:
– ProtTest is quite slow. Many iterations may be needed to obtain a fitting model.

See Github Issues for more details:

–

Authors:
– Dario D’Auria (Founder)
– Dino Danan (Maintainer)
– Guido D’Incà (Contributor)
– Giuseppe Vitale (Contributor)
– Hector Rubiales (Contributor)
– Mike Rychlak (Contributor)
– Marco Bardi (Contributor)
– Enrico Betta (Contributor)
– David Firth (Contributor)
– Javier Lucio (Contributor)
– Franco Donatelli (Contributor)
– Frederik Fourie (Contributor)
– István Horváth (Contributor)
– Pierpaolo Sorrentino (Contributor)
– Pradeep Sreenivasan (Contributor)
– Roberto Zenaro (Contributor)
– Alexander Gromov (Contributor)
– Nicolas Blin (Contributor)
– Elia Santin (Contributor)
– Yingchao Yang (Contributor)
– Zhuang Ni (Contributor)
– Aurélien Buge (Contributor)
– Bernhard Steiner (Contributor)
– Fulvio Tomasi (Contributor)
– Sylvain Raimbault (Contributor)
– Damyan Shyanykov (Contributor)
– Sergio Poggi (Contributor)
– Yun-Tao Liu (Contributor)

Join the NGTO initiative and collaborate on issues and pull-requests with the group!

Contribut

ProtTest Keygen Full Version [32|64bit]

The Akaike Information Criterion (AIC) is a measure of the quality of a statistical model used to estimate parameters from a set of data (for example, evolutionary rates). Akaike defined the AIC as,

where is the number of parameters in the model, the observed information (measures the accuracy of the model) and is the model complexity (adds power to the model).

ProtTest Crack Keygen solves the optimization problem and minimizes the AIC of the candidate models. It is estimated through the program ProtTest, which is freely available for download at

ProtTest is distributed under the GNU GPL license.

Download ProtTest:

Command line usage (as of 1.0.0):

ProtTest -C {FILE} [options]

Options:

-H – Print the command line usage.

-p – Print training results. By default this option prints the following information about model comparison:
1. -logL – the AICc value for each model (for the best model, the lowest)
2. -lnL – the model log-likelihood for each model (for the best model, the highest)
3. -nSites – the number of sites in the alignment
4. -sD – the degrees of freedom for the assumed model
5. -w – for the best model, the total number of sites in the alignment
(not really needed, but very helpful)

ProtTest is distributed under the GNU GPL license.

Get ProtTest:

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ProtTest Crack+ [Win/Mac]

ProtTest is a freely available, cross platform software package which utilises Bayesian information criterion, Akaike information criterion, and other statistical analyses to compare amino acid substitution models and choose the model with the best fit. There are six substitution models to choose from: WAG, LG, DCMut, JTT, VT and MtREV, which all have slightly different theoretical distributions for amino acid substitution. In addition, it is possible to add ‘+X’ models to the model list for amino acids and the insertion/deletion model of I and D can be considered. It is also possible to add the K + I + G substitution model. Akaike information criterion (AIC), Akaike’s information criterion with extra free parameters (AICc), Bayesian information criterion (BIC) and Deviance information criterion (DIC) are applied to compare models, and all available models are presented to the user. Moreover, it is possible to apply any of the six substitution models or the ‘+X’ to input sequences. Subsequently, the likelihood ratio test of model are performed, and likelihood values of models that are being compared are displayed side by side.
Install in Mac OS X Lion and up
Instructions:

To use ProtTest you need a Mac OS X Lion or higher.
Step 1:
Open the terminal, and type ‘installing’.
Step 2:
Now type ‘cd’,
and then type ‘open -a Terminal.app.’
Step 3:
Type’mac_version’, and hit ‘Return’.
Step 4:
Your version should be revealed. You can proceed to the next step.
Step 5:
At this stage you may receive an error stating ‘-bash: opening: No such file or directory’. This can be resolved by signing out of your Apple ID and then signing back in again.
Step 6:
Paste the following to the terminal:’sudo /Developer/Library/PrivateFrameworks/DevToolsCore.framework/Resources/pbxuser-
mac.app/Contents/Resources/pbxucr.sh’
Step 7:
Return to the terminal, and type ‘installing’.
Step 8:
Now type ‘cd’, and then type ‘open -a Terminal.app.’.
Step 9:
Type’mac_version’.
Step 10:

What’s New In ProtTest?

——
ProtTest is a model test analysis of genetic sequences. It selects the best model of protein evolution from among a set of models. The data are a multiple alignment of protein sequences. The models used for the test analysis are, in most cases, based on substitution matrices. The model selection test is based on the Akaike information criterion (AIC). An independent implementation by the authors allows them to employ different evolutionary models or different codon positions (such as codon position 1, 2 or 3; 1-3 or 1-2-3). Try this tool to do just that!
ProtTest Command-Line
——————-
Usage: protest [options] -alignment [options]
Available Models
—————-
mtREV30, WAG+G, WAG+F, WAG+I, JTT+G, JTT+I, VT+I, VT+G, VT+F, CpREV+I, CpREV+G, CpREV+F, RtREV+I, RtREV+G, RtREV+F, MtMam+I, MtMam+G, MtMam+F, MtArt+I, MtArt+G, MtArt+F, HIVb+I, HIVb+G, HIVb+F, HIVw+I, HIVw+G, HIVw+F
Notes
——-
The options -p, -s, -w, -v, -I, -G, -F, -m are the same as for ModelTest.
ProtTest Options
—————-
-alignment
A list of sequences
-o
A one-line output
-o
A one-line output (same as o, see above)
-c
Check for correct output
-s
Also check for sequence number consistency between input and output
-h
Set the number of parallel analysis threads used for the program (default is 2)
-b
Set the number of jobs to be submitted. Should never be set to 1 unless using -s or -s -o
-p
Print an extended header description of the analysis
-w
Print a one-line output file with the sequence names, the number of sequences, and
the characters in the alignment (as single columns separated by spaces)
-v
Reduce the output one-line format, showing the sequence number

System Requirements:

Mac: OS X 10.7 (Lion) or later
Minimum specs: Intel Core 2 Duo, 2.0 GHz
Recommended specs: Intel Core 2 Duo, 2.5 GHz or higher
Memory: 4 GB RAM
Windows: Windows 7, Vista, or XP with Service Pack 3 or later
Pentium 4-200 MHz, 1 GB

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