gda
Table of Contents
GDA
Version 1.1 (7 January 2002)
Computes linkage and hardy-weinberg disequilibrium, some genetic distances, and provides method-of-moments estimators for hierarchical F-statistics.
Program information
- Windows
- Mac OS 10.2.8 and 10.3 (Jaguar and Panther)
Data type handled
- Microsat
- RFLP
- AFLP
- SNP
- Standard (multi-allelic marker)
Input Files
- uses NEXUS file format
GDADATA block
- If a token begins with a single or double quote character, then every character until the next, matching quote character will be treated as a single token. This is useful as a means of putting blank spaces insice poulation or locus lables.
- commands:
- begin
- dimensions:
- number of populations:
npops=2
- number of loci:
nloci=5
- format:
tokens
/notokens
labels
/nolables
interleaved
haploid
missing=?
separator=/
datapoint=standard
- locusallelelabels (optional):
- loci names
- allele names can be provided
- loci will be numbered beginning with 1 if this command is absent
- matrix:
- end of the data for one population is signified by either a comma or the semicolon indicating the end of the matrix command
- end
- not case-sensitive, except in the matrix command (allele named A is treated as being distinct form a)
haploid data
- two ways:
- if all loci are haploid: include the keyword haploid in the format command
- mixture of haploid and diploid data: hapset command is used to specify which loci are haploid
example
- diploid data:
#nexus begin gdadata; [comments are surrounded by square brackets] dimensions npops=2 nloci=3; format missing=? seperator=/; locusallelelabels 1 'pgi 1', 2 'pgi 2', 3 adh / slow fast ; matrix Embudo: indiv_1 A/A 100/100 slow/fast indiv_2 A/A 75 / 90 slow/slow indiv_3 A/a 75/100 fast/Slow indiv_4 A/A 100/100 fast/fast, Black_Mesa: 1 a/a 110/100 fast/slow 2 a/A 75/100 slow/slow 3 a/a 100/100 fast/fast ; end;
- haploid data:
#nexus begin gdadata; dimensions nloci=5 npops=2; format haploid tokens missing=? datapoint=standard; locusallelelabels 1 locus_1 [ / 1 2 3 4], 2 locus_2 [ / 1 2 3 4], 3 locus_3 [ / 1 2 3 4], 4 locus_4 [ / 1 2 3 4], 5 locus_5 [ / 1 2 3 4]; matrix Pop_1: _1_ 4 3 3 3 4 _2_ 4 4 3 3 4 _3_ 4 4 3 3 4 _4_ 4 4 ? 3 4 _5_ 4 4 2 4 4 _6_ 4 4 4 4 4 _7_ 4 4 3 4 4 _8_ 4 4 3 4 4 _9_ 4 4 ? 3 4 10_ 4 4 3 3 4, Pop_2: _1_ 4 4 2 2 4 _2_ 4 3 4 3 4 _3_ 4 4 3 3 4 _4_ 4 4 4 4 4 _5_ 4 3 4 4 4 _6_ 4 4 4 2 4 _7_ 4 4 3 3 4 _8_ 4 4 4 4 4 ; end;
- mixed haploid/diploid data:
#NEXUS [Note: first 5 loci are diploid and last 3 are haploid] begin gdadata; dimensions nloci=8 npops=6; format tokens labels missing=? datapoint=standard; hapset 6-8; locusallelelabels 1 'dip 1', 2 'dip 2', 3 'dip 3', 4 'dip 4', 5 'dip 5', 6 'hap 1', 7 'hap 2', 8 'hap 3' ; matrix Pop1: indiv1 4/4 4/3 4/3 3/3 4/4 3 3 4 indiv2 4/4 4/4 4/3 3/3 4/4 3 3 4 ...
How to cite
- Lewis, P. O., and Zaykin, D. 2001. Genetic Data Analysis: Computer program for the analysis of allelic data. Version 1.0 (d16c). Free program distributed by the authors over the internet from http://lewis.eeb.uconn.edu/lewishome/software.html
gda.txt · Last modified: 2011/07/13 16:54 by heidi