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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




No version available



  • person_outline Christian Schlotterer

Additional information

Publication for ALLelic Imbalance Metre

Allim citations


IDP ASE: haplotyping and quantifying allele specific expression at the gene and gene isoform level by hybrid sequencing

Nucleic Acids Res
PMCID: 5952581
PMID: 27899656
DOI: 10.1093/nar/gkw1076

[…] llim (), MBASED (), Allele Workbench (), QuASAR (), ASEQ (), EMASE () and others (,,). However, either available phased genotypes (e.g. MMSEQ, asSeq and EMASE) or family trio data (e.g. AlleleSeq and Allim) are required for haplotyping using most of these applications. While QuASAR uses solely RNA-seq data, it can only perform ASE analysis at the single SNV level. MBASED is the only currently avai […]


Structure, form, and meaning in the mental lexicon: evidence from Arabic

PMCID: 4673575
PMID: 26682237
DOI: 10.1080/23273798.2015.1048258

[…] hen prefixes and affixes are stripped off, takes on the role of both the root and the pattern in supporting the derivation of surface word forms. Accordingly, an imperfective active verb form like [yuallim] he teaches is not parsed into the prefix ya~, the root {lm} and the word pattern {fa il}, but into the prefix ya and the stem [allim]. This stem is then used as the basic building block to deri […]


Temperature Stress Mediates Decanalization and Dominance of Gene Expression in Drosophila melanogaster

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

[…] erefore, 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 one […]


Intra Specific Regulatory Variation in Drosophila pseudoobscura

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

[…] pecific 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 (, ). […]


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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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