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A Simple solution to quickly run various commands (create a shortcut on your desktop, right click your desktop, run hotkeys.exe)
Very easy to use.
Added default commands:
1-Reload windows explorer
2-Rename files
3-Move to explorer
4-Back up files
5-Download a file from internet
6-Copy a file to a directory
7-Delete a file
8-Create a Shortcut on the Desktop
9-Open a file/folder/URL
10-Open Explorer
11-Maximize Windows
12-Minimize Windows
13-Close a Window
14-Close All Windows
15-Pause
16-Play
17-Record a Macro
18-Stop Macro
19-Save Macro
20-Run Macro
21-Edit Macro
22-Assign Hotkey
23-Show Hotkey List
24-Show Run Menu
25-Show Quick Start Menu
26-Show Toolbar
27-Show Notification Bar
28-Open Script File
29-Run Script
30-Print
31-Go to the next page
32-Go to the previous page
33-Go to home page
34-Go to Tools Page
35-Go to Help Page
36-Go to About page
37-Go to Program Settings
38-Go to About page
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Bayesian analyses are often considered a greater modeling than MML analyses and the Bayesian chains are preferred in phylogenetic analyses. We have collected some hints for the users of MrBayes software in this book. Use these tips if you plan to use MrBayes with, for example, molecular or amino acid data.
Programming Language:
The Bayesian package uses the GNU C++ compiler to run the programs. The package includes the Berkeley B.jar library (jars) as well as the BUGS language, which allows for easy customization of programs.
Programming Language:
Molecular data analyses are typically based on Markov models of molecular evolution. These models are based on the fact that the probability of the substitution between any two sites in a DNA, or protein, or RNA molecule is directly proportional to the rate of exchange between the two sites. Therefore, in a Markov chain model, the probability of a substitution between two different sites at time step n is calculated as:
or 1-cos (pi)n, where pi is the probability of the mutation at a single site.
Programming Language:
The following hints will help you to use this software:
Use the option „Program Bayesian Evolutionary Analysis“
The Bayesian evolutionary analysis software can be used to generate a Bayesian tree in several ways. To run the program, you can set the value „Program Bayesian Evolutionary Analysis“ in the „run“ box. By default, MrBayes program will generate a tree based on the gamma model of rate variation with four discrete rate categories. The option to change the number of rate categories can be found in the graphical user interface.
Use the settings of the program
MrBayes uses three methods for rate heterogeneity across sites: the mixed model, the uncorrelated model, and the gamma model. To run the analysis, the following settings can be found in the program:
Mixed model, the correlation and the proportion of invariable sites can be changed through the „Alphabet size“ options. The method used to calculate the alpha parameter (i.e. gamma vs inverse gamma) can be changed through the „Gamma shape“ options. MrBayes supports the Kimura 2-parameter model of substitution for nucleotide data, the F81 model for amino acid data, and the general time-reversible model for both amino acid and nucleotide data. The relative proportion of invariable sites is estimated by calculating the proportion of sites that are invari

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