ALE reconciliation files

Reconciliation of gene families for the 24 species genomic datasets<br>ml_reconciliations.tar.gz - ALE Maximum Likelihood reconciliations of gene families<br>Trees.tar.xz - ML tree files for all orthogroups<br>ALE_objects.tar.gz - ALE objects generated from tree files<br>alternative_root_trees.tar.gz - Alternative topologies used to test the likelihood of different root positions<br>dated_genome_tree.tre - dated species phylogeny against which gene trees were reconciled<br>alternartive_root_trees.tar.gz - alternative root positions tested using ALE<br>genome_alignment.phy - concatenated sequence alignment used to infer unrooted topology and divergence times<br>genome_set_input.txt - treefile with fossil calibration information for divergence time estimation<br>genome_dated_posterior.tre - treefile containing divergence times of genome-only phylogeny <br>genome_dated_posterior.txt - parameter output of divergence time analysis<br>in.BV - estimated branch lengths and Hessian matrix for divergence time analysis<br>WEREWOLF_loss.newick.txt - gene family phylogeny for WEREWOLF<br>WOX4_loss.newick.txt - gene family phylogeny for WOX4<br>STM_loss.newick.txt - gene family phylogeny for STM<br>

24个物种基因组数据集的基因家族协同校正分析
ml_reconciliations.tar.gz - 基因家族的ALE最大似然协同校正结果
Trees.tar.xz - 所有直系同源组（orthogroup）的最大似然树文件
ALE_objects.tar.gz - 由树文件生成的ALE对象文件
alternative_root_trees.tar.gz - 用于检验不同根位置似然性的备选拓扑结构文件
dated_genome_tree.tre - 用于基因树协同校正的定年物种系统发育树
alternartive_root_trees.tar.gz - 通过ALE检验的不同根位置备选文件
genome_alignment.phy - 用于推断无根拓扑结构与分化时间的串联序列比对文件
genome_set_input.txt - 包含用于分化时间估算的化石校准信息的树文件
genome_dated_posterior.tre - 仅基于基因组数据的系统发育树的分化时间树文件
genome_dated_posterior.txt - 分化时间分析的参数输出文件
in.BV - 用于分化时间分析的估算分支长度与黑塞矩阵文件
WEREWOLF_loss.newick.txt - WEREWOLF基因家族的系统发育树文件
WOX4_loss.newick.txt - WOX4基因家族的系统发育树文件
STM_loss.newick.txt - STM基因家族的系统发育树文件