lamarc
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| lamarc [2007/12/13 16:40] – heidi | lamarc [2008/07/22 13:31] (current) – external edit 127.0.0.1 | ||
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| * Microsatellites | * Microsatellites | ||
| * electrophoretic data | * electrophoretic data | ||
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| ===== Input Files ===== | ===== Input Files ===== | ||
| === LAMARC File Converter: === | === LAMARC File Converter: === | ||
| - | can convert [[PHYLIP]], RECOMBINE and [[MIGRATE]] files to a LAMARC XML file | + | can convert [[PHYLIP]], RECOMBINE and [[MIGRATE]] files to a LAMARC |
| === LAMARC XML file: === | === LAMARC XML file: === | ||
| Line 62: | Line 71: | ||
| * < | * < | ||
| * < | * < | ||
| - | * < | + | * < |
| - | Valid values are site numbers between the value of the offset for that segment (which defaults to 1) and the length of the segment plus the offset. If the segment is longer than the number of markers you have (as is the case for SNP data), valid values here are the same values used for the ' | + | * < |
| + | * sequences themselves | ||
| + | * Each datablock must have an attribute indicating the type of data it contains (type=" | ||
| + | * Sequence data must be aligned and of the same length for all samples within a region | ||
| + | * " | ||
| + | * Upper- and lowercase nucleotide symbols are treated equivalently | ||
| + | * Deletions should be coded as unknown and will be treated as unknown | ||
| + | * Microsatellite data are coded as the number of repeats, with "?" | ||
| + | |||
| + | **examples: | ||
| + | * minimal DNA data block describing a single region, a single segment, a single population, and two individuals with a single haplotype each. Note that while the two blocks of data are differently formatted, they contain the same number of bases; this is required since all blocks corresponding to a single segment: <code xml> | ||
| + | < | ||
| + | <region name=" | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | CTTGTAACCTAATGGCTTCCGAGATGGACTAGTGAGCCGCTTTCTC | ||
| + | TACACCAACGCAGCACATGACGGTCTTACATGCGGAGCCCGCTCAA | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | CTTGTAACCTAATGGCTTCCGA | ||
| + | GATGGACTAGTGAGCCGCTTTCTC | ||
| + | TACACCAACGCAGCACATGACG | ||
| + | GTCTTACATGCGGAGCCCGCTCAA | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | * a microsatellite data block which also illustrates the use of multiple samples per individual. In this example, " | ||
| + | < | ||
| + | <region name=" | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | 7 8 14 7 9 21 | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | 7 9 14 7 9 21 | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | 7 9 14 7 10 23 | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | 8 9 13 7 ? 23 | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
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| ===== How to cite ===== | ===== How to cite ===== | ||
lamarc.1197560433.txt.gz · Last modified: 2008/07/22 13:30 (external edit)