iTree: A high-throughput phylogenomic pipeline

Ahmed Moustafa, Debashish Bhattacharya, Andrew E. Allen

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations

Abstract

Phylogenomics, conventionally defined as the intersection of phylogenetics and genomics, has become a key instrument in a wide spectrum of biological studies, including resolution of complex evolutionary relationships, assignment of taxonomic affiliation, prediction of protein molecular functions, and tracing horizontal gene transfer event. Here, we introduce an open-source phylogenomic pipeline, iTree, which automates the execution of phylogenetic analyses under multithreaded and grid-computing environments, providing a scalable high-throughput platform for performing genome-wide evolutionary analyses. Furthermore, we describe the results of two applications of using iTree: (1) taxonomic assignment of 16S ribosomal RNA sequences from human oral metagenomic samples and (2) detection of horizontal gene transfer in microbial genomes.

Original languageEnglish (US)
Title of host publication2010 5th Cairo International Biomedical Engineering Conference, CIBEC 2010
Pages103-107
Number of pages5
DOIs
StatePublished - Dec 1 2010
Event2010 5th Cairo International Biomedical Engineering Conference, CIBEC 2010 - Cairo, Egypt
Duration: Dec 16 2010Dec 18 2010

Publication series

Name2010 5th Cairo International Biomedical Engineering Conference, CIBEC 2010

Other

Other2010 5th Cairo International Biomedical Engineering Conference, CIBEC 2010
CountryEgypt
CityCairo
Period12/16/1012/18/10

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering

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    Moustafa, A., Bhattacharya, D., & Allen, A. E. (2010). iTree: A high-throughput phylogenomic pipeline. In 2010 5th Cairo International Biomedical Engineering Conference, CIBEC 2010 (pp. 103-107). [5716071] (2010 5th Cairo International Biomedical Engineering Conference, CIBEC 2010). https://doi.org/10.1109/CIBEC.2010.5716071