Detection of positive selection by using Data Monkey server

Screenshot from 2014-02-13 09:51:12The DataMonkey server wraps the HyPhy open-source software package to analyze genetic sequences and infer about molecular evolution.

Website: http://www.datamonkey.org/

Positive selection is one of the major types of natural selection, and occurs when a beneficial mutation occurs in a population and increases in frequency, because increased the fitness.

Methods to evaluate positive selection:

  • FEL (fixed effects likelihood);
  • SLAC (single-likelihood ancestor counting);
  • REL (relaxed effects likelihood).

These three methods are based on dN/dS ratio. The dN/dS (also known Ka/Ks or ω) test calculates the ratio of the rate of nonsynonymous substitutions (dN, the number of nonsynonymous substitutions per nonsynonymous site) to the rate of synonymous substitutions (dS, the number of synonymous substitutions per synonymous site).

Input file for Data Monkey

  • Multiple nucleotide sequence alignment. Click here to get more information about the data formats accepted.

Steps for estimating positive selection:

Access this address www.datamonkey.org

Click on “Analyze your data“. You will be redirected to http://datamonkey.org/dataupload.php.

Screenshot from 2014-02-24 09:48:11

Click on “Choose file”, select your alignment and then click in “upload”.

The next page summarizes your multiple sequence alignment. If there is some stop codons, you must revise your alignment.

Click on “Proceed to the analysis menu” button.

In this page we will execute the “automatic model selection tool” to define a nucleotide substitution model that fits well to your sequences (input file). You can jump this step if you already know the best substitution model for your data.

Click on “Execute” button.

Wait until the Data Monkey server define the nucleotide substitution model.

Wait approximately 60 seconds to see the result:

Screenshot from 2014-05-27 10:53:13

The best model for our hypothetical data is “F81”.

Now, click on the button “[Information: Other Analyses]”, on the right side of Job ID.

Screenshot from 2014-05-27 10:56:45

In this page you can choose the method to calculate positive selection. You must execute only one method by time.

First, lets execute the SLAC method by clicking on the blue [SLAC] button.

Screenshot from 2014-05-27 11:01:32

Select the “F81 nucleotide substitution model” and then click on the button “Click to Run the analysis.”

This process will take approximately 30 seconds. Your result will appear in a next page.

If you think that 0.1 of significance level is too restrictive, you may change 0.5 and click on “Retabulate”.

Screenshot from 2014-05-27 11:08:58

By click on “[Information: Other Analyses]” you are able to perform the other methods to positive selection (FEL and REL).

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