Scientific Publications

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.

Publication TypeJournal Article
AuthorsBansal, MS, Alm EJ, and Kellis M.
AbstractGene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the use of a reconciliation framework, where the input consists of a gene family phylogeny and the corresponding species phylogeny, and the goal is to reconcile the two by postulating speciation, gene duplication, horizontal gene transfer and gene loss events. This reconciliation problem is referred to as duplication-transfer-loss (DTL) reconciliation and has been extensively studied in the literature. Yet, even the fastest existing algorithms for DTL reconciliation are too slow for reconciling large gene families and for use in more sophisticated applications such as gene tree or species tree reconstruction.
Year of Publication2012
JournalBioinformatics (Oxford, England)
Volume28
Issue12
Pagesi283-i291
Date Published (YYYY/MM/DD)2012/06/15
ISSN Number1367-4803
DOI10.1093/bioinformatics/bts225
PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/22689773?dopt=Abstract