The Adaptive Evolution Database

TAED is a database of phylogenetically indexed gene families. It contains multiple sequence alignments from MAFFT1, maximum likelihood phylogenetic trees from PhyML2, bootstrap values for each node, dN/dS ratios for each lineage from the free ratios model in PAML3, and labels for each node of speciation or duplication from gene tree/species tree reconciliation using SoftParsMap4. The phylogenetic indexing enables simultaneous viewing of lineages with high dN/dS that occurred along the same species tree branches. Resources from the Protein Data Bank (PDB) and the Kyoto Encyclopedia of Genes and Genomes (KEGG)5, have been incorporated into the TAED analysis to detect substitutions along each branch within the phylogenetic tree and to assess selection within pathways.

TAED（Taxonomic Assignments of Evolutionary Divergence）是一项基于系统发育学索引的基因家族数据库。该数据库汇聚了来自MAFFT1的多序列比对数据，PhyML2构建的最大似然系统发育树，每个节点处的bootstrap值，以及基于PAML3中的自由比率模型计算得到的每个谱系的dN/dS比率。此外，通过SoftParsMap4对基因树与物种树的调和，为每个物种形成或复制节点标注了标签。系统发育学索引功能使得用户能够同时观察沿同一物种树分支发生的具有高dN/dS比率的谱系。TAED分析还整合了蛋白质数据银行（PDB）和京都基因与基因组百科全书（KEGG）5的资源，以检测系统发育树中每个分支上的替换，并评估通路内的自然选择。