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Fixes Issue JRaviLab#90 -
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 - Refactored  and merged R/tree.R CreateFA2Tree and ConvertFA2Tree.
- Parametrized every hardcoded value and path in ConvertFA2Tree
- Refactored convertAlignment2Trees to support running both modes.
- Backward compatible
- Updated all documentation for R/tree.R
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@Atheriz-46
Atheriz-46 committed Oct 22, 2024
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