Tag: Core Genome

Harvest 1.1.2 – A Suite of Core-genome Alignment and Visualization tools

Harvest 1.1.2

:: DESCRIPTION

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes. Harvest includes: Parsnp, a fast core-genome multi-aligner, Gingr, a dynamic visual platform, and harvest-tools, providing both a reference compressed binary archive and format conversion tools.

::DEVELOPER

The University of Maryland Center for Bioinformatics and Computational Biology (CBCB)

:: SCREENSHOTS

Harvest

:: REQUIREMENTS

  • Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Harvest

:: MORE INFORMATION

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM.
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.
Genome Biol. 2014;15(11):524. doi: 10.1186/s13059-014-0524-x. PMID: 25410596; PMCID: PMC4262987.

CoreAligner – Multiple Genome Alignment for Core Genome Structure Identification

CoreAligner

:: DESCRIPTION

CoreAligner is a software for identifying the core structure of related genomes, which is defined as a set of sufficiently long segments in which gene orders are conserved among multiple genomes so that they are likely to have been inherited mainly through vertical transfer. Using a dynamic programming based algorithm, CoreAligner finds the order of pre-identified orthologous groups (OGs) that retains to the greatest possible extent the conserved gene orders.

::DEVELOPER

Ikuo Uchiyama (uchiyama@nibb.ac.jp)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 CoreAligner

:: MORE INFORMATION

Citation

I. Uchiyama (2008)
Multiple genome alignment for identifying the core structure among moderately related microbial genomes
BMC Genomics, 9:515.