====== PGD: old versions ====== * root element: * 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) \\ * stylesheet: {{stylesheet_data-format3.pdf|}} ===== 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\\