高通量测序微生物多样性流程.pptVIP

Heuristic neighbor-joining Reducing the length of the tree: Nearest-neighbor interchanges Subtree-prune-regraft moves Distance model Maximizing the trees likelihood with NNIs Local support values How it Works FastTree has five stages: Unifrac UniFrac provides a suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample. /unifrac/ Determine if the environments in the input phylogenetic tree have significantly different microbial communities. Determine if community differences are concentrated within particular lineages of the phylogenetic tree. Cluster environments to determine whether there are environmental factors (such as temperature or salinity) that group communities together. Determine whether the environments were sampled sufficiently to support cluster nodes. Visualize the differences between environments graphically. UniFrac allows you to: weighted UniFrac 利用各样品中微生物序列间的进化信息来计算样品间的距离 Weighted UniFrac算法可用于定量beta多样性评估分析 weights the branches based on abundance information during the calculations detect changes in how many organisms from each lineage are present detecting changes in which organisms are present calculate the raw weighted UniFrac value (u) n is the total number of branches in the tree, bi is the length of branch i, Ai and Bi are the number of descendants of branch i from communities A and B respectively, and AT and BT are the total number of sequences from communities A and B respectively. In order to control for unequal sampling effort, Ai and Bi are divided by AT and BT. PCA uses the UniFrac metric to perform principal coordinates analysis on the environments, allowing you to see whether different types of environments are separated in different dimensions. PCoA * * * * 微生物多样性分析流程 余果 2012.8.22 微生物多样性 细菌 真菌