MultiPhATE2: code for functional annotation and comparison of phage genomes

Carol L. Ecale Zhou, Jeffrey Kimbrel, Robert Edwards, Katelyn McNair, Brian A. Souza, Stephanie Malfatti

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)
33 Downloads (Pure)


To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.

Original languageEnglish
Article numberjkab074
Number of pages5
JournalG3 (Bethesda, Md.)
Issue number5
Early online date17 Mar 2021
Publication statusPublished - 7 May 2021


  • bacteriophage
  • bioinformatics tool
  • comparative genomics
  • gene prediction
  • genome annotation
  • phage


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