Ragout

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* 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

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* 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

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* 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

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

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

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* A snapshot of version used in ISMB 2014 paper