Input File Format
Input file for POPGENE analysis consists of the header section and the data. The headersection specifies (1) a job title delimited by /* ... */; (2) number of populations; (3)
number of loci and (4) locus names. The body of data starts with, for each population,population ID # (optional), population name (optional). If you do not give population ID#
or population name, you must leave at least one blank line between populations andPOPGENE will generate population ID # automatically for you. But if you do, yourpopulation ID
# and population name must be unique for each population. The raw data,in free format and with or without one or more spaces between columns, immediatelyfollow without blank
lines in between. Missing values must be set to “ . ‘‘ for haploidsand dominant markers such as RAPDs (i.e., one digit to score for presence or absence ofallele) and “..”
(i.e., two digits) for diploids co-dominant markers in your input file. Hereare three examples of data. The first two datasets have space between columns and thethird dataset
has mixture of space and without space to illustrate flexibility of data inputand how input file for haploid and diploid should be prepared.
Input file format for haploid data
/* Haploid numeric data of 3 populations each with 3 records (gametes) & 19 loci*/
Number of populations = 3
locus name :
AAT-1 AAT-2 ACO ADH APH DIA-2 DIA-3 GDH G6H IDH MDH-1 MDH-2 MDH-3 MDH-4 ME PGIID = 1
1 1 1 2 1 1 1 1 2 1 1 1 2 1 1 1 1 1 1
1 1 1 2 1 1 1 1 2 1 1 1 2 1 1 1 1 1 1
ID = 2
1 1 1 2 1 1 1 1 2 1 1 1 3 1 1 1 1 1 1
1 1 1 1 1 1 1 1 2 1 1 1 6 3 1 1 1 1 1
ID = 3
1 1 3 2 3 1 1 1 1 1 1 1 2 1 1 1 1 1 1
1 1 1 2 3 1 1 1 2 1 1 1 2 1 1 1 1 1 1
Input file format for diploid data, co-dominant marker
/* Diploid alphabetic data of 3 populations each with varying records(genotypes) & 21 loci */
Number of populations = 3
Locus name : AAT-3 ACO ADH DIA-1 DIA-3 EST-2 GDH G6P HAIDH MDH-1 MDH-2 MDH-3 MDH-4 PEP-1 PEP-2 PGI-2 PGM SPG-2AA AA AA AA AA AA AA BB AA AA AA AA AA AA AA AA AA AA
AA AA AAAA AA AA AB BB A3 AA AB BB AA AA AA AA AA AA AA AA AA AB AA AAAA AA AA AA BB CC AA BB AB AA AA AA AA AA AA AA AA AA AA AA AAAA AA AA AA AB AC AA BB AA AA AA AA AA AA AA
AC AA AA AA AB AAAB AA AA AA BC AC AA AB AB AA AA AA AA AB AA AB AA AA AA AA AAAA AA AA AA AA BC AA AB AA AA AA AA AA AA AA AB AA AA AA AA AAAA AA AA AB BC BC AA BB AB AA AA AA
AA AB AA AA AA AA AA AC AAAA AA AA AA AB AC AA BB AA AA AA AA AA AA AA AA AA AA AA AA AAAA AA AA AB AA AC AA AB AB AA AA AA AA AA AA AB AA AA AA AA AAAA AA AA AA BB BB AA AA AA
AA AA AA AA AA AA AB AA AA AA AA AAAA AA AA AB BB BC AA BB AA AC AA AA AA AA AA AA AA AA AC AD AAAA AA AA AA AB BC AA AB AB AA AA AA AA AA AA AA AA AA AA AA AAAA AA AA AA AA BC
AA AB AB AA AA AA AA AA AA BC AA AA AA AA AAAA AA AA AA BD BC AA AB AB AA AA AA AA AA AA AA AA AA AC AE AAAA AA AA AB CC BB AA BB AA AA AA AA AA AA AA AA AA AA AA AB AAAA AA AA
AB CC BB AA AA AB AA AA AA AA AA AA AA AA AA AA AB AAAA AA AA AA AB BC AA AA BB AA AA AA AA AA AA AB AA AA AA AA AAAA AA AA AB AC AB AA BB AA AA AA AA AA AA AA AA AA AA AA AB
AAAA AA AA AB AB AB AA BB AA AA AA AA AA AA AA AA AA AA AA AA AAAA AA AA AA BB AB AA AA AA AA AA AA AA AA AA BB AA AA AA AA AAAA AA AA AA CC BC AA AB AB AA AA AA AA AA AA AB AA
AA AA AC AAAA AA AB AA BE BB AA BB AB AA AA AA AA AA AA AB AA AA AA AA AAAA AA AA AA AB BC AA AB AA AA AA AA AA AA AA AB AA AA AA AA AAAA AA AA AB AC BC AA BB BB AA AA AA AA AA
AA AA AA AA AA AA AAAA AA AA AB BB AC AA BB AA AA AA AA AA AA AA AB AA AA AA AA AAAA AA AA AA AC AC AA AA AB AA AA AA AB AA AA AB AA AA AA AA AAAA AA AA AA BC BC AA BB AB AA AA
AA AA AA AA AB AA AA AA AC AA
Input file format for diploid data, dominant marker/* Diploid RAPD Data Set */
Number of populations = 2
Locus name :1-2 OPA01-3 OPA01-4 OPA01-5
OPA03-1 OPA03-2 OPA03-3 OPA03-4 OPA03-5 OPA03-6OPA04-1 OPA04-2 OPA04-3 OPA04-4 OPA04-5 OPA04-6 OPA04-7OPA11-1 OPA11-2 OPA11-3 OPA11-4
name = Slave Lake
fis = -0.238 0111010 001000 1001
10110 100100 0011010 001000 0001
11111 100100 0011010 001010 0001
10110 101100 0011010 001010 1101
11101 100100 0101010 001000 1001
11001 100100 0111010 001010 1001
11101 101100 0101010 001000 1001
11101 111100 0011010 001000 0001
11000 100100 0000010 001010 0001
11001 100100 0110010 001000 1001
name = Little Smoky
fis = 0.0
11101 111101 0111010 111000 1111
11110 100001 1011010 101010 1011
10101 111111 0011010 111000 0101
11000 100000 0111010 111010 0111
11101 101111 0011010 011010 1001
11011 111100 0011010 011010 1011
11110 111101 0011010 001001 0011
11111 111110 0000010 111010 0111
11101 100000 1111010 001000 1001
11111 100000 1111010 001000 1001
11001 101100 0100010 110100 1001
11001 111000 0010010 001000 0001
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