ALFRED: allele frequency database
      The ALlele FREquency Database   
ALFRED is a resource of gene frequency data on human populations
supported by the U. S. National Science Foundation.

Data Download Format Information

The ALelle FREquency Database (ALFRED) is designed to store and make available allele frequencies of normal, common autosomal DNA polymorphisms in multiple, well defined population samples. The allele frequency data in ALFRED can be downloaded in different formats.
Tab Delimited
ALFRED XML - discontinued
Polymorphism Markup Language (PML) - discontinued

Tab Delimited
A tab delimited allele frequency file will contain the following fields:
popNamePopulation Name
popUIdALFRED UID for Population
sampleUIdALFRED UID for sample
2NNumber of Chromosomes (Sample Size)
locusSymbolGene/Locus Symbol
entryDateDate the data was entered into ALFRED
frequencyAllele frequency data

We have discontinued providing downlodable files in ALFRED XML format. Contact us if you would like to have files in ALFRED XML format for a selected set of sites.
The DTD (Document Type Definition) for ALFRED XML can be downloaded from the
ALFRED Data dump Information page. Researchers can select polymorphic sites they are interested in and download allele frequency data into separate files. Data is also available in single compressed “data dump” file in the declared XML format.

Polymorphism Markup Language (PML)
We have discontinued providing downlodable files in PML format. Contact us if you would like to have files in PML format for a selected set of sites.
ALFRED is part of an international effort organized by JBIC (
Japan Biological Informatics Consortium) to standardize sequence variation data. PML (Polymorphism Markup Language) is the XML implementation of the standardized data exchange schema which can be used for download and upload of sequence variation data in the Life Sciences domain. The specification and XML implementation are approved by OMG and supported by major sequence variation databases. The specification provides definitions for core objects and relationships related to sequence polymorphism in general. It is not tied to a specific implementation and can be used, besides in XML formats, in building other software constructs like databases or application interfaces.

An allele frequency file downloaded in Arlequin format will contain all the allele frequency tables for every population sample typed for the selected site. The downloaded file can be used in Arlequin just by replacing the file extention 'txt' by 'arp'.

© 2019 Kenneth K Kidd, Yale University. All rights reserved. The full Copyright Notification is also available.
Originally prototyped by Michael Osier with the aid of Kei Cheung
Upgrades and maintenance since 2002 by Haseena Rajeevan