gda
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* Windows | * Windows | ||
* Mac OS 10.2.8 and 10.3 (Jaguar and Panther) | * Mac OS 10.2.8 and 10.3 (Jaguar and Panther) | ||
+ | |||
+ | |||
+ | |||
===== Data type handled ===== | ===== Data type handled ===== | ||
- | * DNA Sequences | + | * Microsat |
- | * Protein Sequences | + | * RFLP |
+ | * AFLP | ||
+ | * SNP | ||
+ | * Standard (multi-allelic marker) | ||
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===== Input Files ===== | ===== Input Files ===== | ||
* uses [[NEXUS]] file format | * 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: | ||
+ | * number of loci: '' | ||
+ | * format: | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * 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, | ||
+ | | ||
+ | === 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/ | ||
+ | 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/ | ||
+ | #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 ===== | ===== How to cite ===== | ||
* Lewis, P. O., and Zaykin, D. 2001. Genetic Data Analysis: | * Lewis, P. O., and Zaykin, D. 2001. Genetic Data Analysis: |
gda.1213776454.txt.gz · Last modified: 2008/07/22 13:30 (external edit)