Fix installation and add tree inference vignette#4
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maribraga merged 12 commits intotreeppl:mainfrom Jan 9, 2026
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…ct and rename other functions
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This PR fixes the problem with treeppl installation (the folder treeppl-linux or treeppl-mac has to be created before downloading the self-contained treeppl file).
This PR updates all vignettes. The only remaining problem is with the host repertoire vignette, which will be fixed in the next PR.