II.7 - Agrogenom final reconciliation within orthologous subfamilies and ancestral genome gene content reconstruction

Final step of reconciliation procedure, including the Wagner parsimony reconstruction of ancestral presence/absence states of orthologous subfamilies in ancestral genomes, hereby inferring events of gene gain (by horizontal transfer or origination of the lineage) and loss. These inferences are only based on the phylogenetic profile (i.e. gene presence/absence state in extant genomes) of the subfamily. Note transfers can be inferred, not relying on gene tree topology conflict information but only interpreting the heterogeneous patterns of presence.
The output of ancestral_content.py program here includes:
modified_trees/ folder: reconciled gene tree in phyloXML and serialized Python object (pickle) formats (analogous to content in refined_trees/ folder in item #II.6, updated to final reconciliation step
family_history_pickles/ folder: 41,664 gene family scenarios projected on the species tree, serialized Python object (pickle) format
ortho_subtrees/ folder: 41,664 gene family scenarios and reconciliation (i.e. projected on the species tree and the gene tree, respectiely), broken down by orthologous subfamily
NB: the 41,664 gene families include small gene families (<3 sequences) for which no gene tree was computed and reconciled in the previous pipeline ; for those, only the Wagner parsimony reconstruction is used