INPUT TO DifferInt

• 1. Create a text file containing the genetic data
• 2. Start program
• 3. Enter interactive specifications for running DifferInt

Step 1: Create an input file

Create a text file that contains the genetic data and place it in the same directory as the executable. Two examples:

• exa1.txt and exa2.txt (text file for Linux - Unix format)
• exa1w.txt or exa2w.txt (text file for Windows - DOS format)

Line-by-line description of genetic data input files:

• Line 1: Beginning with "#", name of data
• Line 2: Number of populations
• Line 3: Number of gene loci
• Line 4: "yes", if each line containing a genetic type begins with the count of individuals that possess this genetic type, "no" otherwise
• Line 5: Empty line (optional)
• Line 6: "#" followed by name of population 1 (optional)
• Data for population 1:
  One line of data for each (multilocus) genetic type, as a list of the (numerical!) designations of the two alleles at each of the loci, preceded by count of individuals if Line 4 contains "yes".
  Max. length of lines = 256 characters
  Max. length of allele names = 3 characters
• Empty line
• Line containing "#" followed by name of population 2 (optional)
• Data for population 2 (as for Population 1)
• Empty line
• Continue until data for last population has been entered
• End file by placing cursor at the beginning of the next line

Step 2: Start execution of DifferInt by one of the following methods

• Menu-driven execution:
  
  
  
  • Linux: Enter "./DifferInt" on a command line or click on file "DifferInt" in a data manager
  • Windows: Click on "DifferInt.exe" in a file manager or enter "DifferInt" on a Windows command line

• Keyboard-driven execution:
  
  
  
  • Linux: Enter "./DifferInt -nomenu" on a command line and choose options described in Step 3 by typing on the keyboard the answers to the questions as they appear on the screen
  • Windows: Enter "DifferInt" on a Windows command line and choose options described in Step 3 by typing on the keyboard the answers to the questions as they appear on the screen

• Batch-type execution: Choose options by typing answers to all questions listed in Step 3 into a batch file named e.g. "inspec".
  
  
  
  • Linux: Enter "./DifferInt inspec" on a command line
  • Windows: Enter "DifferInt inspec" on a Windows command line

Step 3: Choose options for DifferInt:

The following description refers to menu-driven execution, but the questions are the same for keyboard-driven and batch-type execution.

Select pre-prepared input file in file select window (text format), then in the new window enter the requested information into the text boxes:

• "List one or more loci for inclusion in multilocus genotypes":
  
  For selection of all loci, retain preselected text "All X loci". Otherwise, replace text by a list of loci by number, separated by blanks or commas. The number of loci in the data is determined by a first reading of the input file.
• Give populations equal weights = 1/No.pops?
  
  An answer of "No" weights populations relative to their numbers of individuals.
• Permute alleles over individuals within populations?
  
  Analyze effects of gene-pools on differentiation.
• Permute individual genotypes among populations?
  
  Analyze effects of gene-pools and gene association on differentiation.
• "Number of permutations for calculation of p-values?":
  
  Insert a large integer, such as 1000.
• "Size of confidence intervals as percentage of permutations":
  
  Either retain preselected value of 95.0% or replace by desired percentage
• "Prefix for names of output files (max.10 characters)?":
  Insert up to 10 characters to designate output files, for example, "xxx"
• "Make snail graphics (using "xfig" software in Linux)?"
  or
  "Make snail graphics (using "WinFig" software in Windows)?":
  
  An answer of "yes" causes preparation of two files for the creation of snail graphics.
  
  For each level of genetic integration, the snails rank the populations as pie pieces of decreasing radius around a central point, where the radius assigned to each population is proportional to the genetic distance of this population to the complement population formed by pooling all other populations [2].
  
  The snails in "xxx.Delta.schnecken-nocj.fig" (for prefix "xxx") reflect the genetic distances Δ_SD(j), which consider the elementary genic differences between genetic types; the snails in "xxx.d0.schnecken-nocj.fig" reflect the genetic distances D(j), which neglect genic differences.
  
  The fig-files serve as input to the vector graphics program "xfig" (Linux) or "WinFig" (Windows), where they can be altered by the user and exported in a number of formats.