This is in response to an e-mail query about how to run a local version of SLAC analyses for positive selection described in Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login.

1. Prepare a codon file with an attached tree string (FASTA,PHYLIP or NEXUS formats)
2. Choose the "Analysis->Standard Analyses" menu option in the GUI versions of HyPhy (or just launch the command line version - a list of standard analyses is displayed by default).
3. Choose Positive Selection class of analyses
4. Select QuickSelectionDetection.bf
5. Choose your genetic code
6. Select 'New Analysis' (see comments below for the other option)
7. Load sequence data 
8. Choose a model of sequence evolution to correct for nucleotide biases. Default is HKY85, otherwise choose custom and type in the model string. See the paper for details. The most general model possible (REV) can be requested as 012345
9. Respond to the tree query
10. Choose the file to save the nucleotide fit to. Later you can reuse that fit by selecting 'Restore' in step 6.
11. Choose "Estimate" option ("Estimate dN/dS only" is faster and almost as good)
12. Choose "Single Ancestor Counting"
13. Wait... the program now does model fitting and prints results to the console
14. Choose "Full Tree"
15. Choose the way to treat ambiguities ("Averaged" is sensible for viral data where ambiguities are likely to be true population mixtures)
16. "Approximate" test statistic
17. Choose significance level. Due to the conservative nature of the test statistic, the rule of thumb can be 0.2 for <=20 sequences, 0.1 <= 50 sequences, 0.05 > 50 sequences. This is also sensitive to the level of divergence.
18. The program will print a summary to the console. E.g.
Code:

******* FOUND 1 POSITIVELY SELECTED SITES ********


+--------------+--------------+--------------+--------------+
| Index	  | Site Index   | dN-dS	  | p-value	|
+--------------+--------------+--------------+--------------+
|		1 |    28.000000 |     3.857121 |     0.134411 |
+--------------+--------------+--------------+--------------+

******* FOUND 4 NEGATIVELY SELECTED SITES ********


+--------------+--------------+--------------+--------------+
| Index	  | Site Index   | dN-dS	  | p-value	|
+--------------+--------------+--------------+--------------+
|		1 |    47.000000 |    -3.758732 |     0.117406 |
+--------------+--------------+--------------+--------------+
|		2 |    61.000000 |    -4.065251 |     0.144961 |
+--------------+--------------+--------------+--------------+
|		3 |    77.000000 |    -2.443241 |     0.147924 |
+--------------+--------------+--------------+--------------+
|		4 |    89.000000 |    -3.815241 |     0.087369 |
+--------------+--------------+--------------+--------------+
 

19. Choose "Chart" with GUI versions (save to file with command line)
20. On GUI versions HyPhy will display a detailed chart with all the quantities inferred by the analyses (see paper for details on what they are).
You can save this chart for later viewing with HyPhy, or export to CSV for a spreadsheet program.

HTH,
Sergei