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Commits on Sep 8, 2023

• Merge pull request #5 from JennKnapp/main

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• Correction to Clade 4 mutations.

  

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  eecc19d

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• Merge pull request #4 from JennKnapp/main

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• Fixed a typo in lineages.py and analyze.py

  

  JennKnapp

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  8fe4110

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• Merge pull request #3 from JennKnapp/main

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• Merge branch 'main' of github.com:JennKnapp/altob into main

  

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• Corrected and updated clade definitions.

  

  JennKnapp

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• Merge pull request #2 from JennKnapp/main

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• Correct frame of mutations in clades 1, 2, 6, 7, 8

  

  JennKnapp

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Commits on Jul 11, 2023

• Merge pull request #1 from JennKnapp/main

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Commits on Jul 5, 2023

• Merge branch 'main' of github.com:JennKnapp/altob into main

  

  JennKnapp

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  0e186bd

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• Updated clade definitions

  

  JennKnapp

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  b2e922c

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• Update README.md

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Commits on Jun 21, 2023

• Updated clade definitions based on a re-made tree

  

  JennKnapp

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Commits on Jun 15, 2023

• Updated prep.py to be specific to altob

  

  JennKnapp

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• Updated reference sequence to KT383474, made new clade constellations

  

  JennKnapp

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Commits on Jun 9, 2023

• Fixed mutation used as a key to get the list of clades

  

  JennKnapp

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  6a45e9a

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• Updating root genome and pulling muts from nodes of tree

  

  JennKnapp

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Commits on Mar 29, 2023

• Update to be consistent with alcov

  

  JennKnapp

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  3f5c8b0

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Commits on Feb 13, 2023

• Updating altob to match alcov updates

  

  JennKnapp

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Commits on Jun 1, 2022

• Default to use shared, don't plot residuals

  Ellmen

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• Default to max 100%

  Ellmen

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Commits on May 24, 2022

• Calling ToBRFV clades

  Ellmen

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Commits on May 10, 2022

• Alcov -> Altob

  Ellmen

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• Almost ready for alcov2

  Ellmen

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Commits on Apr 4, 2022

• Save mutation heatmaps

  Ellmen

  committed
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Commits on Mar 25, 2022

• Optionally save lineage heatmap

  Ellmen

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  a86d9c7

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• Positional arguments

  Ellmen

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• Updated mutation lists, linear programming approach

  Ellmen

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Commits on Feb 10, 2022

• Show colour bar, percentages in lineage heatmap

  Ellmen

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Commits on Feb 3, 2022

• For now, ignore mutations after a deletion

  Ellmen

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Commits on Feb 2, 2022

• Add new options to README

  Ellmen

  committed
  1b7da71

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• Big update: new lineages, option for only uniqe mutations, new visualizations, more customization

  Ellmen

  committed
  259329c

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• Support DEL:x syntax

  Ellmen

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  3087c0d

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• Update lineage, mutation data

  Ellmen

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