convert
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convert [2007/12/20 16:18] – heidi | convert [2008/09/10 13:26] (current) – heidi | ||
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===== Program information ===== | ===== Program information ===== | ||
* Windows 95/ | * Windows 95/ | ||
+ | |||
===== Data type handled ===== | ===== Data type handled ===== | ||
- | * co-dominant, | + | * co-dominant, |
+ | * Microsat | ||
+ | * RFLP | ||
+ | * SNP (numeric) | ||
+ | * Standard | ||
+ | * AFLP | ||
+ | |||
+ | |||
+ | |||
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===== Input (read) formats ===== | ===== Input (read) formats ===== | ||
- | * Excel file | ||
* [[GENEPOP]] | * [[GENEPOP]] | ||
+ | * Excel file: | ||
+ | * first line (cell A1): brief description of the data file | ||
+ | * second line (cell A2): number of populations present in the data file (e.g.: '' | ||
+ | * third line (cell A3): number of loci (e.g.: '' | ||
+ | * fourth line: names of the loci (in order, without spaces, underscores are allowed) | ||
+ | * Each population starts with the line '' | ||
+ | * Each individual within a population begins with an individual name (can be numeric, not allowed: '/', | ||
+ | * After an individual’s name, the diploid genotypes are given for that individual: | ||
+ | * on the same line or wrapped to the next line | ||
+ | * alleles must be given in numeric form (two alleles for each locus) | ||
+ | * They can be any integer between 1 and 9999 | ||
+ | * Typically the numbers will indicate the size of the allele in base pairs (e.g., for microsats) | ||
+ | * Missing data: '?' | ||
+ | * Creating a text input file from the EXCEL file: ' | ||
+ | *example: < | ||
+ | Canucks vs Yanks for the Ice Hockey gold - Salt Lake City 2002 | ||
+ | |||
+ | npops = 2 | ||
+ | nloci = 4 | ||
+ | SSR01 SSR02 SSR03 SSR04 | ||
+ | pop = Canadian_Team | ||
+ | |||
+ | Lemieux 239 245 204 222 169 185 180 206 | ||
+ | Sakic 241 247 216 238 195 195 174 198 | ||
+ | Fleury ? | ||
+ | Kariya 229 239 226 240 181 203 182 194 | ||
+ | Yzerman 223 239 224 226 191 195 174 180 | ||
+ | Lindros 237 245 222 226 179 193 194 222 | ||
+ | pop = American_Team | ||
+ | |||
+ | Chelios 235 243 216 226 179 183 172 218 | ||
+ | Leetch 235 239 208 216 179 191 198 208 | ||
+ | Suter 237 241 222 224 185 197 166 192 | ||
+ | Housley ? | ||
+ | Hatcher 237 241 222 222 173 187 160 198 | ||
+ | Amonte 235 245 226 230 181 181 178 192 | ||
+ | </ | ||
+ | |||
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===== Outfile (write) formats ===== | ===== Outfile (write) formats ===== | ||
- | * GDA | + | * [[GDA]] |
* [[GENEPOP]] | * [[GENEPOP]] | ||
* [[Arlequin]] | * [[Arlequin]] | ||
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* can produce a summary table of allele frequencies in which private alleles and the sample sizes at each locus are indicated | * can produce a summary table of allele frequencies in which private alleles and the sample sizes at each locus are indicated | ||
- | ===== How to cite ===== | ||
+ | ===== How to cite ===== | ||
+ | Glaubitz J.C. (2004) CONVERT: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Molecular Ecology Notes 4: 309-310. |
convert.1198163928.txt.gz · Last modified: 2008/07/22 13:30 (external edit)