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Allegro specifications


Unique identifier OMICS_09410
Name Allegro
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained Yes


No version available

Publications for Allegro

Allegro citations


A Homozygous LAMA2 Mutation of c.818G>A Caused Partial Merosin Deficiency in a Japanese Patient

PMCID: 5891531
PMID: 29225264
DOI: 10.2169/internalmedicine.9588-17

[…] polymorphisms (SNP) genotypes of the proband and his mother using Genome-Wide Human SNP array 6.0 (Affymetrix, Santa Clara, USA), a parametric linkage analysis was performed using SNP-HiTLink () and Allegro version 2 (). A region on chromosome 6 flanked by rs567564 and rs9386195, which includes the LAMA2 locus, showed a positive LOD score with runs of homozygous SNPs (). A copy number analysis us […]


Prevalence of spinocerebellar ataxia 36 in a US population

PMCID: 5515602
DOI: 10.1212/NXG.0000000000000174
call_split See protocol

[…] es and not shared by genotyped controls in families A and B (), multifamily parametric linkage analysis was conducted using a fully penetrant dominant model with no phenocopies (f0,1,2 = 0,1,1) using ALLEGRO. Logarithm of the odds (LOD) scores generated from linkage in these families are unable to meet genome-wide significance thresholds because of power (max LOD given the information across the p […]


A deep intronic CLRN1 (USH3A) founder mutation generates an aberrant exon and underlies severe Usher syndrome on the Arabian Peninsula

Sci Rep
PMCID: 5431179
PMID: 28469144
DOI: 10.1038/s41598-017-01577-8
call_split See protocol

[…] inkage analysis was performed assuming autosomal-recessive inheritance, full penetrance, consanguinity, and a disease gene frequency of 0.0001. Multipoint LOD scores were calculated using the program Allegro. Haplotypes were reconstructed with Allegro and presented graphically with HaploPainter. Regions of homozygosity by descent (HBD) were annotated with their positions corresponding to NCBI Buil […]


Retinoic acid catabolizing enzyme CYP26C1 is a genetic modifier in SHOX deficiency

PMCID: 5167135
PMID: 27861128
DOI: 10.15252/emmm.201606623
call_split See protocol

[…] r related samples were deleted. Non‐parametric linkage analysis using all genotypes of a chromosome simultaneously was carried out with MERLIN.Parametric linkage analysis was performed by the program ALLEGRO (Gudbjartsson et al, ), assuming dominant inheritance with complete penetrance and a disease allele frequency of 0.0001. Haplotypes were reconstructed with ALLEGRO and presented graphically wi […]


FAT1 mutations cause a glomerulotubular nephropathy

Nat Commun
PMCID: 4770090
PMID: 26905694
DOI: 10.1038/ncomms10822
call_split See protocol

[…] metric logarithm of odds (LOD) scores were calculated using a modified version of the program GENEHUNTER 2.1 (refs , ) through stepwise use of a sliding window with sets of 110 SNPs using the program ALLEGRO. Genetic regions of homozygosity by descent (‘homozygosity peaks') were plotted across the genome as candidate regions for recessive disease-causing genes as described. Disease allele frequenc […]


Mutation in ATG5 reduces autophagy and leads to ataxia with developmental delay

PMCID: 4786408
PMID: 26812546
DOI: 10.7554/eLife.12245.017

[…] he Qiagen (Germantown, MD) Gentra Puregene isolation kit. Linkage analysis was performed using the genotype data generated with Illumina HumanOmniExpress-24 chip for the mother and the four sibs. The Allegro module () of easyLINKAGE software was used, assuming autosomal recessive inheritance and parents as third cousins. No deletion or duplications common to just the two affected brothers were det […]


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Allegro institution(s)
Decode Genetics, Lynghals, Reykjavik, Iceland; Institute of Statistics and Decision Sciences, Duke University, Durham, NC, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA

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