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ALCHEMY specifications


Unique identifier OMICS_03511
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for ALCHEMY

ALCHEMY in publications

PMCID: 5668218
PMID: 29098463
DOI: 10.1186/s12284-017-0186-x

[…] raw hybridization intensity data processing was performed using the genotyping module in the beadstudio package (illumina, san diego, ca, usa), followed by allele calling using alchemy software (wright et al. ). graphical genotyping of both ir29 and hasawi was performed using flapjack ( software developed by the scottish crop research […]

PMCID: 4415243
PMID: 25895682
DOI: 10.1186/s12863-015-0199-7

[…] was compared by one-way anova using minitab v14.0 (minitab inc.). the verascan raw data from beadxpress reader was initially analyzed using the genomestudio software v1.1.0 (illumina co.) and alchemy []. the generated report and map file were used for qtl analysis by using composite interval mapping (cim) in qgene v4.3.8 []. the genetic distance between snp markers was estimated […]

PMCID: 4092238
PMID: 25076836
DOI: 10.1007/s11032-013-0012-0

[…] software on the beadxpress reader system. raw intensity data were analysed using the genotyping module (v1.6.3) of the illumina genomestudio (v2010.1) software. genotype calling was performed using alchemy software package (wright et al. )., simple statistics of each trait and correlation coefficient between the traits were computed using phenotypic means. the linkage map was constructed using […]

PMCID: 4455769
PMID: 24760390
DOI: 10.1534/g3.114.010561

[…] sequence tags and sequenced pcr amplicons, derived principally from one wild barley accession and eight malting barley cultivars, primarily from europe and the united states ()., the program alchemy () was used to generate machine-scored, automated genotype calls. the program incorporates estimated inbreeding coefficients for each sample to improve accuracy of genotype estimation. unlike […]

PMCID: 3473070
PMID: 23077503
DOI: 10.1371/journal.pone.0046267

[…] genotypes aa, ab and bb. still these methods have to accept a ‘no call’ for some snps, due to high uncertainty., a second approach is to cluster all snps on single arrays, using a mixture model. alchemy does de novo calling for small sets of samples. for each allele it introduces one-dimensional mixtures of normal distributions, one component for noise (when the allele is absent) […]

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ALCHEMY institution(s)
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA

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