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old_versions

PGD: old versions

  • root element: <PGD>
  • microsat data are number of repeats
  • nucleotid data: just one loci in one tag (popLoci/ indLoci)! (If more than one loci: repeat the whole ind tag for every loci)


1. version:


data type
block subtags standard DNA SNP Microsattelite RFLP (AFLP) Allel frequency
header (attribute: title) number_samples x x x x x x
data_type x x x x x x
number_loci number x x x x x
loci (attribute: name) locations o o o o o
length o o o o o
missing o o o o o
gap o o o o o
gametic_phase o o o o o
recessive_alleles o o o o o
sample (attribute: name) size x x x x x x
id (attribute: name) frequency x x x x x x
loci (attribute: name) (when unaligned) position o o o
genotype/haplotype (a) x(a) x(a) x(a)
genotype/haplotype (a) (attribute: name) (when aligned) x x(a) x(a) x x(a)
structure (attribute: name) number_groups o o o o o
group (attribute: name) (sample name, sample name) o o o o o
distance_matrix (attribute: name) size o o o o o
lables o o o o o
matrix o o o o o

x: obligatory
o: optional
a: alternative


2. version:


data type
block subtags standard DNA SNP Microsattelite RFLP (AFLP) Allel frequency
header (attribute: title) number_population x x x x x x
data_type x x x x x x
number_loci* number x x x x x
loci (attribute: name) locations o o o o o
length o o o o o
missing o o o o o
gap o o o o o
gametic_phase o o o o o
recessive_alleles o o o o o
population (attribute: name) size x x x x x x
geographic_coord o o o o o o
id (attribute: name) (a3) frequency x x x x x x
loci (attribute: name) (when unaligned) location o o o
begin o o o
length o o o
genotype/haplotype (a1) x (a1) x (a1) x (a1)
genotype/haplotype (a1) (attribute: name) (when aligned) x x (a1) x (a1) x x (a1)
ind (attribute: name) (a3) geographic_coord o o o o o o
loci (attribute: name) (when unaligned) location o o o
begin o o o
length o o o
genotype/haplotype (a2) x (a2) x (a2) x (a2)
genotype/haplotype (a2) (attribute: name) (when aligned) x x (a2) x (a2) x x (a2)
structure (attribute: name) number_groups o o o o o
group (attribute: name) (sample name, sample name) o o o o o
distance_matrix (attribute: name) size o o o o o
lables o o o o o
matrix o o o o o

* when for all populations the same
x: obligatory
o: optional
a: alternative to


3. version:


data type
block subtags standard DNA SNP Microsattelite RFLP (AFLP) Allel frequency
header (attribute: title) number_populations x x x x x x
data_type x x x x x x
number_loci * number x x x x x
loci (attribute: name) location o o o o o
length o o o o o
gene_copies * x x (a1) x (a1) x x (a1)
aligned x x x x x
genotypic_data x x x x x
missing x x x x x
gap x x x x x
gametic_phase o o o o o
recessive_alleles o o o o o
population (attribute: name) size x x x x x x
geographic_coord o o o o o o
linguistic_group o o o o o o
id (attribute: name) (a3) frequency x x x x x x
genotype/haplotype (attribute: name) x x x x x
ind (attribute: name) (a3) geographic_coord o o o o o
linguistic_group o o o o o
loci (attribute: name) (when unaligned) location o o o
begin o o o
length o o o
gene_copies x (a1) x (a1) x (a1)
genotype/haplotype (a2) x (a2) x (a2) x (a2)
genotype/haplotype (a2) (attribute: name) (when aligned) x x (a2) x (a2) x x (a2)
structure (attribute: name) number_groups o o o o o o
group (attribute: name) (sample name, sample name, …) o o o o o o
distance_matrix (attribute: name) size o o o o o o
labels o o o o o o
matrix (number (line break) number, number (line break)…) o o o o o o

* when for all populations the same
x: obligatory
o: optional
a: alternative to


4. version:


data type
block subtags standard DNA SNP Microsattelite RFLP (AFLP) Allel frequency
header (attribute: title) number_populations x x x x x x
data_type x x x x x x
number_loci * number x x x x x
loci (attribute: name) location o o o o o
length o o o o o
number_strains * x x (a1) x (a1) x x (a1)
aligned x x x x x
genotypic_data x x x x x
missing x x x x x
gap x x x x x
gametic_phase o o o o o
recessive_alleles o o o o o
population (attribute: name) aligned (a2) size x x x x x x
geographic_coord * o (a4) o (a4) o (a4) o (a4) o (a4) o
linguistic_group * o (a5) o (a5) o (a5) o (a5) o (a5) o
number_strains * o (a1) o (a1) o (a1) o (a1) o (a1)
id (attribute: name) (a3) frequency x x x x x x
genotype/haplotype (attribute: name) (loci, loci,…) x x x x x
ind (attribute: name) (a3) geographic_coord o (a4) o (a4) o (a4) o (a4) o
linguistic_group o (a5) o (a5) o (a5) o (a5) o (a5)
number_strains x (a1) x (a1) x (a1) x (a1) x (a1)
genotype/haplotype (attribute: name) (loci, loci,…) x x x x x
population (attribute: name) unaligned (a2) size x x x
geographic_coord * o (a6) o (a6) o (a6)
linguistic_group * o (a7) o (a7) o (a7)
loci_location (attribute: name) * o (a8) o (a8) o (a8)
number_strains * o (a9) o (a9) o (a9)
ind (attribute: name) geographic_coord o (a6)*3 o (a6)*3 o (a6)*3
linguistic_group o (a7)*3 o (a7)*3 o (a7)*3
loci_location (attribute: name)*2 o (a8)*3 o (a8)*3 o (a8)*3
number_strains x (a9) x (a9) x (a9)
strain (attribute: name) begin x x x
length x x x
genotype/haplotype x x x
structure (attribute: name) (o) number_groups x x x x x x
group (attribute: name) (sample name, sample name, …) x x x x x x
distance_matrix (attribute: name) (o) size x x x x x x
labels x x x x x x
matrix (number (line break) number, number (line break)…) x x x x x x

* when for all populations/individuals the same
*2 if it exist –> align DNA over one individual, if it not exist –> align DNA over one population
*3 if for one individual defined, it has to be defined for all individuals
x: obligatory
o: optional
a: alternative to


5. version:


data type
block subtags standard DNA SNP Microsattelite RFLP (AFLP) Allel frequency
header (attribute: title) nb_pop x x x x x x
data_type x x x x x x
loci (o) * nb x x x x x
locus (attribute: id) location x x x x x
length o o o o o
links o o o o o
nb_reads * x (a1) x (a1) x (a1) x (a1) x (a1)
aligned x x x x x
geno_data x x x x x
missing x x x x x
gap x x x x x
gametic_phase o o o o o
recessive_alleles o o o o o
loci (o) nb x x x x x
locus (attribute: id) location x x x x x
length o o o o o
links o o o o o
population (attribute: name) aligned, same data type (a2) size x x x x x x
geo_coord * o (a4) o (a4) o (a4) o (a4) o (a4) o
linguistic_group * o (a5) o (a5) o (a5) o (a5) o (a5) o
nb_reads * x (a1) x (a1) x (a1) x (a1) x (a1)
loci (locus, locus,…) * x x x x x
id (attribute: name) (a3) freq x x x x x x
geno/hap (attribute: name) (locus, locus,…) x x x x x
ind (attribute: name) (a3) geo_coord o (a4) o (a4) o (a4) o (a4) o
linguistic_group o (a5) o (a5) o (a5) o (a5) o (a5)
nb_reads x (a1) x (a1) x (a1) x (a1) x (a1)
geno/hap (attribute: name) (locus, locus,…) x x x x x
population (attribute: name) unaligned (a2) size x x x
geo_coord * o (a6) o (a6) o (a6)
linguistic_group * o (a7) o (a7) o (a7)
locus (attribute: id)* o (a8) o (a8) o (a8)
nb_reads * o (a9) o (a9) o (a9)
ind (attribute: name) geo_coord o (a6)*3 o (a6)*3 o (a6)*3
linguistic_group o (a7)*3 o (a7)*3 o (a7)*3
locus (attribute: id)*2 o (a8)*3 o (a8)*3 o (a8)*3
nb_reads x (a9) x (a9) x (a9)
read (attribute: name) start x x x
length x x x
geno/hap x x x
structure (attribute: name) (o) number_groups x x x x x x
group (attribute: name) (sample name, sample name, …) x x x x x x
distance_matrix (attribute: name) (o) size x x x x x x
labels x x x x x x
matrix (number (line break) number, number (line break)…) x x x x x x

* when for all populations/individuals the same
*2 if it exist –> align DNA over one individual, if it not exist –> align DNA over one population
*3 if for one individual defined, it has to be defined for all individuals

x: obligatory
o: optional
a: alternative to


6. version:


data type
block subtags standard DNA SNP Microsattelite RFLP (AFLP) Allel frequency
header (attribute: title) organism o o o o o o
numPop x x x x x x
numReads * x x x x x
aligned x x x x x
missing x x x x x
gap x x x x x
gameticPhase o o o o o
recessiveData o o o o o
loci (o) lociNum x x x x x
lociDataType * x (a10) x (a10) x (a10) x (a10) x (a10) x
locus (attribute: id) locusDataType a10 a10 a10 a10 a10
locusChromosom o o o o o
locusLocation o o o o o
locusGenic o o o o o
locusLength o o o o o
locusLinks o o o o o
locusComments o o o o o
population (attribute: name) aligned, same data type (a2) popSize x x x x x x
popGeogCoord * o (a4) o (a4) o (a4) o (a4) o (a4) o
popLingGroup * o (a5) o (a5) o (a5) o (a5) o (a5) o
popNumReads * x (a1) x (a1) x (a1) x (a1) x (a1)
popLoci (locus, locus,…) * x x x x x
ind (attribute: name) (a3) indGeogCoord o (a4) o (a4) o (a4) o (a4) o
indLingGroup o (a5) o (a5) o (a5) o (a5) o (a5)
indNumReads a1 a1 a1 a1 a1
indFreq (absolute Freq) o o o o o x
data (locus, locus,…) x x x x x
population (attribute: name) aligned, diff data type (a2) popSize x x x x x
popGeogCoord * o (a4) o (a4) o (a4) o (a4) o (a4)
popLingGroup * o (a5) o (a5) o (a5) o (a5) o (a5)
popNumReads * x (a1) x (a1) x (a1) x (a1) x (a1)
ind (attribute: name) (a3) indGeogCoord o (a4) o (a4) o (a4) o (a4) o
indLingGroup o (a5) o (a5) o (a5) o (a5) o (a5)
indLoci (locus, locus,…) x x x x x
indNumReads a1 a1 a1 a1 a1
indFreq (absolute Freq) o o o o o x
data (locus, locus,…) x x x x x
population (attribute: name) unaligned (a2) popSize x
popGeogCoord * o (a6)
popLingGroup * o (a7)
popNumReads * x (a9)
popLocus * o (a8)
ind (attribute: name) indGeogCoord o (a6)
indLingGroup o (a7)
indLocus *2 o (a8)
indFreq (absolute Freq) o
indNumReads a9
read start x (if unalig.)
length o
data x
structure (attribute: name) (o) numGroups x x x x x x
group (attribute: name) (sample name, sample name, …) x x x x x x
distanceMatrix (attribute: name) (o) matrixSize x x x x x x
matrixLabels (name, name,…) x x x x x x
matrix (number (line break) number, number (line break)…) x x x x x x

* when for all populations/individuals the same
*2 if it exist –> align DNA over one individual, if it not exist –> align DNA over one population

x: obligatory
o: optional
a: alternative to

old_versions.txt · Last modified: 2008/11/24 09:55 by heidi