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Commits on Feb 5, 2022

• Updated the documentation

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• ALL.filterGeneFamilies-size.py can use gene lists in case the ancGenes don't cover the extant species

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• Fixed the documentation

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Commits on May 23, 2021

• Introduced agora-generic.py

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• They were still using the term "scaffolding"

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• Multi-pass second integration

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Commits on May 2, 2021

• typos

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• Being pairs, they are very short !

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• We try to avoid the term "scaffolding"

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• Part of the core Python 3 distribution

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• How-To

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Commits on Jan 6, 2021

• Updated the How-To

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• Changed robust to constrained

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Commits on Dec 7, 2020

• Changed robust to constrained

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Commits on Dec 6, 2020

• Renamed some references to "diags" files

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• Renamed ancDiags to ancBlocks

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• Renamed the integrDiags directory to ancBlocks

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Commits on Nov 20, 2020

• Contiguous Ancestral Region -> Ancestral Genome

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Commits on Nov 19, 2020

• Renamed src/buildSynteny.integr-groups.py -> src/buildSynteny.integr-scaffolds.py

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• Renamed src/buildSynteny.integr-extend.py -> src/buildSynteny.integr-fusion.py

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• Renamed src/buildSynteny.integr-halfinsert.py -> src/buildSynteny.integr-insertion.py

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• Renamed src/buildSynteny.integr-refine.py -> src/buildSynteny.integr-fillin.py

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• Renamed agora2.py to agora-vertebrates.py and agora-robust.ini to agora-vertebrates.ini

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• Renamed agora1.py to agora-basic.py and agora.ini to agora-basic.ini

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Commits on Sep 10, 2020

• New syntax - update this commit message

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Commits on Jun 26, 2020

• HowTo updates

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Commits on Jun 25, 2020

• Changed back the default value of onlySingletons to what it was in the first version

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Commits on Jun 21, 2020

• Mention that lzma/xz support is not out of the box

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Commits on Jun 8, 2020

• HowTo update

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Commits on Jun 3, 2020

• HowTo update

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Commits on May 13, 2020

• HowTo update

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Commits on May 12, 2020

• HowTo update

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• Removed the phylTree files from the example dataset

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Commits on May 5, 2020

• Emphasis on the Newick and NHX files since they are now supported

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• Moved all the conversion scripts to src/ with a new naming scheme

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