title: BIR Pipeline for Preparation of Phylogenomic Data.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  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.
authors.affiliation: Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Epigenetics, Development and Evolution (CEDE), Department of Biosciences, University of Oslo, Norway.
authors.forename: Surendra
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Epigenetics, Development and Evolution (CEDE), Department of Biosciences, University of Oslo, Norway.
authors.forename: Anders K
authors.initials: AK
authors.lastname: Krabberød
authors.affiliation: Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Epigenetics, Development and Evolution (CEDE), Department of Biosciences, University of Oslo, Norway.
authors.forename: Ralf S
authors.initials: RS
authors.lastname: Neumann
authors.affiliation: Research Computing Services, University of Oslo, Oslo, Norway.
authors.forename: Katerina
authors.initials: K
authors.lastname: Michalickova
authors.affiliation: Genome Biology Group, Department of Caner Prevention, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
authors.forename: Sen
authors.initials: S
authors.lastname: Zhao
authors.affiliation: Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Epigenetics, Development and Evolution (CEDE), Department of Biosciences, University of Oslo, Norway.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Epigenetics, Development and Evolution (CEDE), Department of Biosciences, University of Oslo, Norway.
authors.forename: Kamran
authors.initials: K
authors.lastname: Shalchian-Tabrizi
keywords: alignment construction; genomics; ortholog prediction; phylogenetics; phylogenomics; transcriptomics