gda
Differences
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gda [2008/06/18 11:09] – heidi | gda [2011/07/13 16:54] (current) – heidi | ||
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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 ===== | ||
- | * AFLP........ | + | |
+ | * RFLP | ||
+ | | ||
+ | * SNP | ||
+ | * Standard (multi-allelic marker) | ||
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===== Input Files ===== | ===== Input Files ===== | ||
* uses [[NEXUS]] file format | * uses [[NEXUS]] file format | ||
+ | |||
==== GDADATA block ==== | ==== GDADATA block ==== | ||
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* commands: | * commands: | ||
* begin | * begin | ||
- | * dimensions | + | * dimensions: |
- | * format | + | * number of populations: |
- | * locusallelelabels | + | * number of loci: '' |
- | * matrix | + | * format: |
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * locusallelelabels | ||
+ | * 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 | * 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 === | === example === | ||
- | < | + | * diploid data: < |
#nexus | #nexus | ||
Line 56: | Line 85: | ||
; | ; | ||
end; | 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 | ||
+ | ... | ||
</ | </ | ||
gda.1213780148.txt.gz · Last modified: 2008/07/22 13:30 (external edit)