II.4 - Agrogenom first integration of reconciliation scenarios

10,774 annotated gene trees in phyloXML and serialized Python oblect (pickle) formats, and associated database records describing the duplication and transfer events inferred in these reconciled gene trees.
Obtained using Python script rec_to_db.py from pre-reconciled gene trees (see item #II.2) and the results of Prunier HGT inference on unicopy subtrees (see item #II.3).
Prunier-inferred transfers are mapped back to the full gene tree, and reconciliations are completed using taxonomic incongruency scoring and DL parsimony to assign transfer or duplication events to the relevant nodes

本数据集包含10774条经注释的基因树，格式涵盖phyloXML与序列化Python对象（pickle），同时附带关联的数据库记录，用于描述这些协调基因树中所推断出的基因重复与水平基因转移事件。
该数据集通过Python脚本rec_to_db.py，基于预协调基因树（详见条目II.2）以及Prunier工具在单拷贝子树上的水平基因转移（Horizontal Gene Transfer, HGT）推断结果（详见条目II.3）构建得到。
将Prunier工具推断出的转移事件映射回完整基因树，随后通过分类学不一致性评分与DL简约法完成协调分析，将转移或重复事件分配至对应的节点处。