GraphML specializations for ancestral recombinant graphs

Frontiers in Genetics

Mary eKuhner¹  Elizabeth eWalkup¹  James eMcGill¹ 

[1] University of Washington, department of Genome Sciences;

关键词: XML;    ancestral recombination graph;    GraphML;    ARG;    Newick;   

DOI  :  10.3389/fgene.2013.00146

来源: DOAJ

【 摘 要 】

Software which simulates, infers, or analyzes ancestral recombination graphs (ARGs) faces the problem of communicating them.Existing formats omit information either about the location of recombinations along the chromosome or the position of recombinations relative to the branching topology.We present a specialization of GraphML, an XML-based standard for mathematical graphs, for communication of ARGs.The GraphML type is specialized to contain the node type, time, recombination location, and name. The GraphML type is specialized to contain the ancestral material passed along that edge.This approach, which we call ArgML, retains all information in the original ARG.Due to its use of established formats ArgML can be parsed, checked and displayed by existing software.

【 授权许可】

Unknown