WH Software

WH is a handy computer program designed to fit a speciation model and check how well that model works. The specific model it uses is called the Isolation Model, which means it looks at species that don't mix genes. By comparing DNA sequences from two closely related species, this software can help you figure out how long ago those species split and how big their common ancestor was.

How the Isolation Model Works

The Isolation Model makes a few key assumptions:

• There are two species or populations sampled from one common ancestor that existed t generations ago.


• The ancestral population had a constant size called NA.


• The two descendant populations have sizes N1 and N2.


• The population sizes stay constant except when they split.


• No gene flow happens between the two populations after they separate.


• All mutations are neutral (they don't affect survival).

Getting Started with WH

You'll want to keep your program file in the same folder as your data file or in a place your operating system checks automatically. Running the program is simple! You can do it through command line parameters or just type in the name of the program, which is 'wh'. If you skip using parameters, it will ask you for what you need at runtime.

User-Friendly Operation

If you're starting up on a PowerPC, clicking on the program icon opens a small window where you can enter command line parameters. But if you want, just hit return, and WH will ask for basic info instead!

Command Line Parameters Explained

If you're using command line options, here's what to type:

wh -d'datafilename' -r'resultsfilename' -N'numsims' -L'ldtype' -A'ranseed'

This breaks down like this:

• 'datafilename': This should be in the same folder as WH.


• 'resultsfilename': This is where results will be saved with a '.wh' extension.


• 'numsims': This tells how many simulations to run; basic fitting doesn't need this.


• 'ldtype': This indicates what linkage disequilibrium value to calculate; ensure your data supports this option.
  
  
  
  • 'R': correlation coefficient
  
  
  • 'S': square of the correlation coefficient (r²)
  
  
  • 'D': basic gametic disequilibrium measure D
  
  
  • 'P': D' value calculation based on maximum possible D given observed allele frequencies
  
  
  • 'B': absolute value of D |D|
  
  
  
  

'ranseed': A random number seed that's optional unless you want to repeat simulations exactly. Need more info? Check out our detailed guide at Softpas.com!