Ragout 2.3

• Python 3 support
• A few minor bugs fixed

Ragout 2.2

• Migration to networkx 2.2 (thanks to @latticetower)

Ragout 2.1.1

• Improved installation scripts for better system integration

Ragout v 2.1

• Various small bigfixes and improvements
• Better compatability with Bioconda packages

Ragout v2.0

• The support of large genomes if finally stable
• Fixes in scaffold gaps estimations
• maf2synteny module updated
• Assembly graph refinement is now disabled by default
• Various improvements and bugfixes

Ragout v1.2

• A significant improvement in missassmblies detection
• New output format: NCBI AGP
• Output of unplaced input sequences into a separate file
• Scaffolds naming wrt to reference genomes
• "Links" format changed a bit
• "Circular" option is deprecated
• Various improvements and bugfixes

Ragout v1.1

• Added optional repeat resolution algorithm
• Automatic phylogenetic tree inference
• Automatic inference of the synteny block scale
• Recipe syntax changed a bit
• New synteny backend: HAL alignment
• Progressive Cacuts and MAF backennds are deprecated (use HAL instead)
• Various improvements and bugfixes

Ragout v1.0

First stable release!

• New "links" output format with detailed information about adjacencies
• Refine option is enabled by default
• Manuals improved
• Various fixes

Ragout v0.3b

• Moving from Python package back to simple "python code + native binaries" format
• Changed recipe syntax
• Estimation of distances between contigs
• Various improvements

Ragout v0.2b

This version was used in ISMB 2014 paper.