polysat: an R package for polyploid microsatellite analysis
We present an R package to help remedy the lack of software for manipulating and analysing autopolyploid and allopolyploid microsatellite data. polysat can handle genotype data of any ploidy, including populations of mixed ploidy, and assumes that allele copy number is always ambiguous in partial he...
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| Veröffentlicht in: | Molecular ecology resources 2011-05, Vol.11 (3), p.562-566 |
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| container_title | Molecular ecology resources |
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| creator | CLARK, LINDSAY V JASIENIUK, MARIE |
| description | We present an R package to help remedy the lack of software for manipulating and analysing autopolyploid and allopolyploid microsatellite data. polysat can handle genotype data of any ploidy, including populations of mixed ploidy, and assumes that allele copy number is always ambiguous in partial heterozygotes. It can import and export genotype data in eight different formats, calculate pairwise distances between individuals using a stepwise mutation and infinite alleles model, estimate ploidy based on allele counts and estimate allele frequencies and pairwise FST values. This software is freely available through the Comprehensive R Archive Network (http://cran.r-project.org/) and includes a thorough tutorial. |
| doi_str_mv | 10.1111/j.1755-0998.2011.02985.x |
| format | Article |
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It can import and export genotype data in eight different formats, calculate pairwise distances between individuals using a stepwise mutation and infinite alleles model, estimate ploidy based on allele counts and estimate allele frequencies and pairwise FST values. 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It can import and export genotype data in eight different formats, calculate pairwise distances between individuals using a stepwise mutation and infinite alleles model, estimate ploidy based on allele counts and estimate allele frequencies and pairwise FST values. This software is freely available through the Comprehensive R Archive Network (http://cran.r-project.org/) and includes a thorough tutorial.</description><subject>allele copy number ambiguity</subject><subject>alleles</subject><subject>allopolyploidy</subject><subject>autopolyploidy</subject><subject>Computational Biology - methods</subject><subject>computer software</subject><subject>data conversion</subject><subject>exports</subject><subject>FST</subject><subject>gene frequency</subject><subject>Gene loci</subject><subject>genetic distance</subject><subject>Genotype</subject><subject>Genotype & phenotype</subject><subject>heterozygosity</subject><subject>Mathematical Computing</subject><subject>Microsatellite Repeats</subject><subject>mutation</subject><subject>Polyploidy</subject><subject>Software</subject><subject>SSR</subject><issn>1755-0998</issn><issn>1755-098X</issn><issn>1755-0998</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkVtv1DAQhS0Eohf4CxCJB54SZuz1DcQD6g1EWySgwNvIyTqVt9km2Lti99_jkLJCPNUvHmm-c-w5w1iBUGE-rxYVailLsNZUHBAr4NbIavOA7e8aD_-p99hBSgsABVbPHrM9jjODHOU-ezP03Ta51evC3Rafi8E1N-7aF20fi7EzdH2YF8vQxD5DvuvCymfSZU1IT9ij1nXJP727D9nV6cnXo_fl-aezD0fvzstGSiVLoWVta-WxFQJU4-1cqgas5EarmfK88bJGNJ67WnhoZQNQc4uybQ1XVtfikL2cfIfY_1z7tKJlSE3-jLv1_TqRUVoLpQDvQaI22VNk8sV_5KJfxzxYIpSoZygkjJSZqHH-FH1LQwxLF7eEQOMmaEFjyDSGTOMm6M8maJOlz-4eWNdLP98J_0afgbcT8Ct0fntvY7o4uRyrrC8nfUgrv9npXbwhpXPm9P3yLFsdf_v441TTReafT3zrenLXMSS6-pKdJQBobq0UvwFAia0k</recordid><startdate>201105</startdate><enddate>201105</enddate><creator>CLARK, LINDSAY V</creator><creator>JASIENIUK, MARIE</creator><general>Blackwell Publishing Ltd</general><general>Wiley Subscription Services, Inc</general><scope>FBQ</scope><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SN</scope><scope>7SS</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201105</creationdate><title>polysat: an R package for polyploid microsatellite analysis</title><author>CLARK, LINDSAY V ; 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| identifier | ISSN: 1755-0998 |
| ispartof | Molecular ecology resources, 2011-05, Vol.11 (3), p.562-566 |
| issn | 1755-0998 1755-098X 1755-0998 |
| language | eng |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | allele copy number ambiguity alleles allopolyploidy autopolyploidy Computational Biology - methods computer software data conversion exports FST gene frequency Gene loci genetic distance Genotype Genotype & phenotype heterozygosity Mathematical Computing Microsatellite Repeats mutation Polyploidy Software SSR |
| title | polysat: an R package for polyploid microsatellite analysis |
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