Allegro protocols

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Allegro statistics

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Associated diseases

Associated diseases

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


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Publications for Allegro

Allegro in pipelines

PMCID: 3567443
PMID: 23023333
DOI: 10.1038/ng.2425

[…] markers for fine mapping were identified using the ucsc human genome browser and were synthesized with fluorescent-labels (sigma-genosys). two point and multipoint lod scores were calculated using allegro, assuming recessive inheritance with full penetrance and a disease allele frequency of 0.001. sequencing primers were designed using primer3, and genomic dna was sequenced using standard […]

PMCID: 3575525
PMID: 22801503
DOI: 10.1038/nature11280

[…] dna sequencing. a plasmid map is shown in ., linkage peaks were identified by subjecting dna to genome-wide genotyping using the affymetrix 10k snp arrays and analyzed using the software application allegro v.2.0 to generate multi-point lod scores. only affected members (and married-in samples) were used for the analysis. targeted exome capture and deep sequencing was accomplished using a exome […]

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Allegro in publications

PMCID: 5774751
PMID: 29351342
DOI: 10.1371/journal.pone.0191224

[…] affymetrix was used. nonparametric lod scores were calculated using a modified version of the program genehunter 2 through stepwise use of a sliding window with sets of 110 snps [,]. the program allegro was employed to identify regions of homozygosity by descent as described using a disease allele frequency of 0.0001 and ceu marker allele frequencies []., genomic dna (2 μg) from the affected […]

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 […]

PMCID: 5515602
DOI: 10.1212/NXG.0000000000000174

[…] 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 […]

PMCID: 5454394
PMID: 28589169
DOI: 10.1002/acn3.417

[…] using genotyping console 4.0 (affymetrix). parametric multipoint linkage analysis (autosomal recessive model with complete penetrance) was conducted using the pipeline software snp‐hitlink and allegro version 2 employing single‐nucleotide polymorphisms (snps) satisfying a p > 0.001 in the hardy–weinberg test, a call rate of >0.98, a genotyping confidence score of <0.02, a minor […]

PMCID: 5431179
PMID: 28469144
DOI: 10.1038/s41598-017-01577-8

[…] 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 […]

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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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