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Kumar S, Krabberød AK, Neumann RS, et al. BIR Pipeline for Preparation of Phylogenomic Data. Evol Bioinform Online. 2015;11:79-83doi: 10.4137/EBO.S10189.
Kumar, S., Krabberød, A. K., Neumann, R. S., Michalickova, K., Zhao, S., Zhang, X., & Shalchian-Tabrizi, K. (2015). BIR Pipeline for Preparation of Phylogenomic Data. Evolutionary bioinformatics online, 1179-83. https://doi.org/10.4137/EBO.S10189
Kumar, Surendra, et al. "BIR Pipeline for Preparation of Phylogenomic Data." Evolutionary bioinformatics online vol. 11 (2015): 79-83. doi: https://doi.org/10.4137/EBO.S10189
Kumar S, Krabberød AK, Neumann RS, Michalickova K, Zhao S, Zhang X, Shalchian-Tabrizi K. BIR Pipeline for Preparation of Phylogenomic Data. Evol Bioinform Online. 2015 Apr 27;11:79-83. doi: 10.4137/EBO.S10189. eCollection 2015. PMID: 25987827; PMCID: PMC4412416.
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Evol Bioinform Online. 2015 Apr 27;11:79-83. doi: 10.4137/EBO.S10189. eCollection 2015.

BIR Pipeline for Preparation of Phylogenomic Data.

Evolutionary bioinformatics online

Surendra Kumar, Anders K Krabberød, Ralf S Neumann, Katerina Michalickova, Sen Zhao, Xiaoli Zhang, Kamran Shalchian-Tabrizi

Affiliations

  1. Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Epigenetics, Development and Evolution (CEDE), Department of Biosciences, University of Oslo, Norway.
  2. Research Computing Services, University of Oslo, Oslo, Norway.
  3. Genome Biology Group, Department of Caner Prevention, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.

PMID: 25987827 PMCID: PMC4412416 DOI: 10.4137/EBO.S10189

Abstract

SUMMARY: We present a pipeline named BIR (Blast, Identify and Realign) developed for phylogenomic analyses. BIR is intended for the identification of gene sequences applicable for phylogenomic inference. The pipeline allows users to apply their own manually curated sequence alignments (seed) in search for homologous genes in sequence databases and available genomes. BIR automatically adds the identified sequences from these databases to the seed alignments and reconstruct a phylogenetic tree from each. The BIR pipeline is an efficient tool for the identification of orthologous gene copies because it expands user-defined sequence alignments and conducts massive parallel phylogenetic reconstruction. The application is also particularly useful for large-scale sequencing projects that require management of a large number of single-gene alignments for gene comparison, functional annotation, and evolutionary analyses.

AVAILABILITY: The BIR user manual is available at http://www.bioportal.no/ and can be accessed through Lifeportal at https://lifeportal.uio.no. Access is free but requires a user account registration using the link "Register for BIR access" from the Lifeportal homepage.

Keywords: alignment construction; genomics; ortholog prediction; phylogenetics; phylogenomics; transcriptomics

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