II.2 - Agrogenom intermediary result files: detection of potential paralogous lineages

File set as generated by find_ancestral_duplications.py program:modified_trees/:<br>Gene trees are modified where branch supports were low and SPR moves allowed to decrease the amount of duplication and loss events; saved as Newick trees.normed_trees/:the same trees saved in custom phyloXML format including the reconciliation information.<br>treeshelves/:<br>the same annotated tree as serialized Python objects.subfams/:lists of (posibly overlapping) unicopy leaf sets extracted from gene families<br>subtrees/:unicopy_subtrees extracted from the (modified) gene trees, the leaf labels only bear the species label; saved as Newick trees.subtree2leaves/:dictionary of subfamily leaf sets to the corresponding subtree files.

本文件集由find_ancestral_duplications.py程序生成，各子目录详情如下：
modified_trees/：当基因树的分支支持度较低时，会对其进行调整，并允许使用SPR（Subtree Pruning and Regrafting，子树剪接重接）操作以降低重复事件与丢失事件的总数量，最终以Newick格式保存修改后的基因树。
normed_trees/：存放与modified_trees/目录中同批次修改后的基因树完全一致的数据集，但采用自定义phyloXML格式存储，且包含基因树调和信息。
treeshelves/：存放经过功能注释的基因树，以序列化Python对象的形式进行持久化存储。
subfams/：包含从各基因家族中提取的（可能存在重叠的）单拷贝叶集合的列表文件。
subtrees/：存放从（经修改的）基因树中提取的单拷贝子树，此类子树的叶节点标签仅保留物种标识，且以Newick格式保存。
subtree2leaves/：存储亚家族叶集合与对应子树文件映射关系的字典文件。