lamarc
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lamarc [2007/12/13 13:34] – 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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contains the actual molecular data, and additional information used to interpret it | contains the actual molecular data, and additional information used to interpret it | ||
* enclosed in < | * enclosed in < | ||
+ | * < | ||
+ | * divides molecular data into " | ||
+ | * available genetic information that is closely linked on the same chromosome and has a known map | ||
+ | * Use multiple regions for data composed of several disconnected bits or bits whose connections are not known | ||
+ | * region' | ||
+ | * < | ||
+ | * specify a different relative effective population size for each < | ||
+ | * < | ||
+ | * Information about the relative position of segments | ||
+ | * < | ||
+ | * Each segment is indicated by this tag | ||
+ | * give information about the position of the segment itself and the positions of the markers within the segment | ||
+ | * < | ||
+ | * < | ||
+ | * < | ||
+ | * < | ||
+ | * < | ||
+ | * Within each region you can list various populations | ||
+ | * 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 | ||
+ | </ | ||
+ | </ | ||
+ | </ | ||
+ | </ | ||
+ | </ | ||
+ | </ | ||
+ | </ | ||
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lamarc.txt · Last modified: 2008/07/22 13:31 by 127.0.0.1