lamarc
Differences
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| lamarc [2007/12/13 13:59] – 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: === | ||
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| * if you list < | * if you list < | ||
| * < | * < | ||
| + | * < | ||
| + | * < | ||
| + | * < | ||
| + | * 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 | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| - | | ||
lamarc.1197550747.txt.gz · Last modified: 2008/07/22 13:30 (external edit)