Checks the tree in the .mod file for internal node labels and exits with an error if they don't exist. This addresses #48 and various other issues where this has been a problem (e.g. #45)
Adds functionality to --labeltree to provide labels in the form of [descendant 1]-[descendant 2], akin to the tree_doctor command we recommended before
Added -iqtree-path and -coal-cmd path when estimating --theta internally
Added some dev options
Better handling of Warnings
Added the --dollo option which re-enables the Dollo assumption from the original model, since this PR includes changes to the PhyloAcc binaries to disable it by default (with the addition of INIT_LRATE2, HYPER_LRATE2_A, and HYPER_LRATE2_Boptions, which are now also options available with the -phyloacc catch-all param
This PR contains commits that:
.modfile for internal node labels and exits with an error if they don't exist. This addresses #48 and various other issues where this has been a problem (e.g. #45)--labeltreeto provide labels in the form of [descendant 1]-[descendant 2], akin to thetree_doctorcommand we recommended before-iqtree-pathand-coal-cmdpath when estimating--thetainternally--dollooption which re-enables the Dollo assumption from the original model, since this PR includes changes to the PhyloAcc binaries to disable it by default (with the addition ofINIT_LRATE2,HYPER_LRATE2_A, andHYPER_LRATE2_Boptions, which are now also options available with the-phyloacccatch-all param