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CHANGELOG.md

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  • Version 1.3.9:
    • TreeShrink works with R 4.0
  • Version 1.3.8b: (unstable)
    • Use Scipy stats instead of R to compute thresholds.
    • Experiments show that the number of species removed at each alpha value may change, but the effect of filtering on gene tree discordance remain the same.
  • Version 1.3.7:
    • Fixed the error in the message when -x is specified.
  • Version 1.3.6:
    • Allow exception species via -x. These species will NOT be removed in any tree.
  • Version 1.3.5:
    • Read each tree instead of using Dendropy TreeList to save memory
    • Decomposition by long branches
    • Allow mutiple-copy gene trees and gene-to-species mapping via -g
    • Output summary file
  • Version 1.3.4:
    • Set recursion depth to 5000
    • Remove internal labels in pruned trees
    • Allow output prefix and allow outputing to an existing folder
    • Add --force to force overriding existing files
    • Add option to show version
    • Show help message if no argument is provided
    • Prevent conversion to scientific form
  • Version 1.3.3:
    • Suppress quotes around dashes in the output trees
  • Version 1.3.2:
    • Suppress quotes around underscores in the output trees
  • Version 1.3.1:
    • If output directory is empty, do not complain
  • Version 1.3.0:
    • Major change: Make -s 2,5 the default. Default k was too big for many datasets.
  • Version 1.2.4:
    • Add ability to adjust default k formula (-s)
    • Output species sorted, to help comparisons
    • New early fail checks
  • Version 1.2.3:
    • Minor bug fix: make sure zero diameter doesn't cause error; just a warning.
  • Version 1.2.2:
    • Made sure .idx files are not created in the target directory. Instead, they reside in temp dir
    • Don't write alignments to temp files.
    • Change logging messages a bit
    • Make sure all temps are in the same folder, and are all kept or removed at the end.
  • Version 1.2.1:
    • Made sure anaconda works
  • Version 1.2.0:
    • Major change: by default, no species will be removed during the per-species test if their impact on diameter is less than 5%. Option -b can be used to change the default behavior.