Arboretum (version 2.4)

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How to compile the executable

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type "make" in the arboretum directory.

  cd arboretum/
  make

The executable will be named arboretum.

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How to get the usage description

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You can obtain the usage for this version with

  ./arboretum --help

Detail description for the input arguments is available at README.txt

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Differences / Key debugging log

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• Addition of the usage of fixed covariance values
  • commented as "FIXED COVARIANCE" in the code.

• Repopulating the ancestral information at the allspecies_clusterassign_lca_brk.txt file
  • commented as "repop" in the several parts of the code.

• Allowance of very small cluster (previously the program ignored clusters < 10 genes)
  • commented as "neuron MODIFICATION" in SpeciesClusterManager.C

• DEBUG: gene tree misusing issue (found by Jon Ide)
  • commented as "JI mod" in GeneTreeManager.C

• DEBUG: fixation of "remove the whole OG" message (Feb 27 2021)
  • code changes GammaManager.C and Expert.C

• DEBUG: fixation of disappearing genes in the final result (Apr 4 2021)
  • code changes GammaManager.C

• DEBUG: fixation for mergeData issue (Aug 19 2021)
  • commented as "source spc only, 210819" in Framework.C