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Merge branch 'devel' into path_cover
Ragout 1.2 (?? Aug 2015) ======================== * A significant improvement in missassmblies detection inside input sequences * New output format: NCBI AGP * Output of unplaced input sequences in a separate file * Output scaffolds naming wrt to reference chromosome names * "Links" format changed a bit * "Circular" option is deprecated * Various improvements and bugfixes Ragout 1.1 (22 Mar 2015) ================ * 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 1.0 (07 Aug 2014) ===================== * First stable release * New "links" output format with detailed information about adjacencies * Refine option is enabled by default * Manuals improved * Various fixes Ragout 0.3b (22 Jun 2014) ====================== * Moving from Python package back to simple "python code + native binaries" format * Changed recipe syntax * Estimation of distances between contigs * Various improvements Ragout 0.2b (25 Apr 2014) ====================== * A snapshot of version used in ISMB 2014 paper Ragout 0.1b (15 Jan 2014) ====================== * First beta release