II.8 - Agrogenom synthesis of genome evolution scenarios

Finalisation of the reconciliation procedure by recomputing the block events based on the final event set and summarizing of ancestral states and events from each gene (sub)family into a pangenome-wide synthesis of species evolutionary history.<br>The event block reports are analogous to the output of step #II.5; the previous and final block set are mostly overlapping, and block_ids of identical blocks are preserved across these sets.<br>The genome history synthesis is generated by ancestral_content.py script ; note it could be done within the same run as as ancestral content reconstruction (previous step #II.7). The output notably includes:- <i>synthesis/</i> folder: - <i>genome_synthesis.*</i> files: species tree annotated with the sum of events (duplication, transfer, origination, loss, replacement) and of gene counts over all families, in extended Newick format (with bracketed comments at nodes) and as a serialized Python object (pickle) - <i>genome_*_synthesis.nhx</i> files: idem but separating annotation of gene count (states) and event count - <i>phylogenetic_profiles/</i> folder: tables of state count per gene family or orthologous subfamily, and by species tree node (any or extant nodes = "leaf" only)<br> - <i>annottables/</i> folder: tables of orthologous gene subfamilies specifically gained/lost at a species tree node, or specifically present/absent in a clade, with the list of corresponding genes in extant genomes, their coordinates and their functional annotation.<br>- <i>ortho_subfam_*.tab</i> files: tables of orthologous subfamilies assignation of gene sequence identifiers or of unique event identifiers, respectively.<br> - <i>specific_gene_dump.tab</i> file: relational database table dump listing the specific gene sets (see <i>annottables/</i> folder)<br> - <i>phylogenetic_profile_dump.tab</i> file: relational database table dump listing presence/absence states of (sub)families at each species tree node (see - <i>phylogenetic_profiles/</i> folder<i>)<br></i>- <i>reconciliation_collection/</i> folder: updated and final set of reconciled gene trees in phyloXML and serialized Python object (pickle) formats.<br><br>