type "make" in the arboretum directory.
cd arboretum/
make
The executable will be named arboretum.
You can obtain the usage for this version with
./arboretum --help
Detail description for the input arguments is available at README.txt
- 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