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We introduce IMPUTOR, software for phylogenetically aware imputation of missing haploid nonrecombining genomic data. Targeted for next-generation sequencing data, IMPUTOR uses the principle of parsimony to impute data marked as missing due to low coverage. Along with efficiently imputing missing variant genotypes, IMPUTOR is capable of reliably and accurately correcting many nonmissing sites that represent spurious sequencing errors. Tests on simulated data show that IMPUTOR is capable of detecting many induced mutations without making erroneous imputations/corrections, with as many as 95% of missing sites imputed and 81% of errors corrected under optimal conditions. We tested IMPUTOR with human Y-chromosomes from pairs of close relatives and demonstrate IMPUTOR's efficacy in imputing missing and correcting erroneous calls.
Pubmed ID: 29722813
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Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. It works along with the Open Bioinformatics Foundation, who generously host it''s website, bug tracker, and mailing lists. Sponsor: This resource is supported by the Open Bioinformatics Foundation. Keywords: Tool, Software, Python, Biological, Computation, Bioinformatics,
View all literature mentionsSoftware program for phylogenetic analyses of large datasets under maximum likelihood.
View all literature mentionsWeb phylogeny server based on the maximum-likelihood principle.
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