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Allim specifications


Unique identifier OMICS_05504
Name Allim
Alternative name ALLelic Imbalance Metre
Software type Application/Script, Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A file for each parent RNA-Seq data or a file for each parent genomic DNA sequencing data and a file containing the reference genome; or a file for each parent genome; or a file including hybrid RNA-Seq; or a file with reference gene annotation.
Output data Some expression tables for allele specific expression on the gene and the exon level or an allelic imbalance test with FDR corrected p-values.
Operating system Unix/Linux, Mac OS
Programming languages Python, R
License Mozilla Public License version 2.0
Computer skills Advanced
Version 1.2
Stability Stable
Biopython, PICARD, SAMTOOLS, BedTools, GSNAP, NumPy, RPy, car, multcomp, edgeR, limma
Maintained Yes



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  • person_outline Christian Schlotterer <>

Additional information

Publication for ALLelic Imbalance Metre

Allim in publications

PMCID: 4342254
PMID: 25719753
DOI: 10.1371/journal.pgen.1004883

[…] we excluded 15 genes with simulated allelic expression divergence to avoid biased divergence estimation caused by mapping errors. the protocols described above are implemented in the package allim []., finally we filtered for a minimum expression level using the following criteria. a gene is defined as expressed in the f0 flies if in all samples at least one read was mapped and at least […]

PMCID: 3873948
PMID: 24386226
DOI: 10.1371/journal.pone.0083547

[…] expression in hybrids., finally, we normalized the expression data using the tmm method . the pipeline described above to identify allele-specific gene expression analysis is implemented in the allim software package (, )., cis- and trans-effects were estimated by contrasting gene expression in the parental and f1 libraries. in order to test for significance […]

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Allim institution(s)
Institut fur Populationsgenetik, Vetmeduni Vienna, Vienna, Austria; Institut fur Evolution und Biodiversitat, Universitat Munster, Munster, Germany; Institut fur Statistik, University of Vienna, Vienna, Austria
Allim funding source(s)
Supported by the Austrian Science Funds (FWF) grant P22834 and by the Volkswagen Foundation.

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