种系进化树分析和构建工具R工具包S

a. 删除物种分支： prune.phylo(file, species)

b. 裁剪物种分支的范围： crop.phylo(file, start, end)

c. 在物种分支上添加标签： label.phylo(file, labels)

d. 提取物种分支的信息： extract.phylo(file, column)

物种分支数据的导出：

a. 导出为NEXUS格式： export.nexus(file, output)

b. 导出为Newick格式： export.newick(file, output)

具体使用方法

S.PhyloMaker是一个用于处理系统发育数据的R工具包。它可以从原始数据中创建系统发育树，并进行一系列的数据处理和可视化操作。下面是使用步骤和常用命令的介绍：

步骤：

1. 安装R：首先需要安装R语言环境，可以从R官方网站(https://www.r-project.org/)下载对应系统的安装包进行安装。
2. 安装S.PhyloMaker：打开R控制台，在命令行中输入以下命令来安装S.PhyloMaker包：

install.packages("S.PhyloMaker")

1. 加载S.PhyloMaker包：在R控制台中输入以下命令来加载S.PhyloMaker包：

library(S.PhyloMaker)

1. 创建系统发育树：

• 使用原始数据创建系统发育树：

tree <- phylo_maker(data = mydata, type = "raw")

这里，mydata是原始数据，type参数指定数据类型为"raw"。

• 从已有的系统发育树文件创建系统发育树：

tree <- phylo_maker(data = "tree_file.nwk", type = "tree")

这里，tree_file.nwk是已有的系统发育树文件路径，type参数指定数据类型为"tree"。

1. 数据处理和分析：

• 提取叶子节点和内部节点：

leaves <- get_leaves(tree)
nodes <- get_nodes(tree)

• 计算节点的度：

degree <- get_degree(tree)

• 计算节点的高度：

height <- get_height(tree)

• 计算节点的深度：

depth <- get_depth(tree)

• 进行系统发育相关的分析：

phylotools_analysis(tree)

1. 数据可视化：

• 绘制系统发育树：

plot_tree(tree)

• 绘制节点度的分布图：

plot_degree(tree)

• 绘制节点高度的分布图：

plot_height(tree)

github使用示例

library("phytools") # load the "phytools" package.
example<-read.csv("example.splist.csv",header=T) # read in the example species list.
phylo<-read.tree("PhytoPhylo.tre") # read in the megaphylogeny.
nodes<-read.csv("nodes.csv",header=T) # read in the nodes information of the megaphylogeny.
result<-S.PhyloMaker(spList=example, tree=phylo, nodes=nodes) # run the function S.PhyloMaker.
str(result) # the structure of the ouput of S.PhyloMaker.
par(mfrow=c(1,3),mar=c(0,0,1,0)) # show the phylogenies of the three scenarios.
plot(result$Scenario.1,cex=1.1,main="Scenarion One")
plot(result$Scenario.2,cex=1.1,main="Scenarion Two")
plot(result$Scenario.3,cex=1.1,main="Scenarion Three")

S.PhyloMaker完成分析脚本（有动手能力的可以改改）：

S.PhyloMaker<-function (tree, spList, nodes, output.spList = T, scenarios = c("S1", "S2", "S3")) 
{
    options(scipen=999)
    tree0 <- tree
    spList[sapply(spList, is.factor)] <- lapply(spList[sapply(spList, is.factor)], as.character)
    if (any(duplicated(spList$species))) 
      {
        warning("Duplicated species detected and removed.")
        print(spList$species[duplicated(spList$species)])
      }
    spList <- spList[!duplicated(spList$species), ]
    spList.original <- spList
    spList$species <- gsub(" ", "_", spList$species)
    spList$species <- gsub("(^[[:alpha:]])", "\\U\\1", spList$species, perl = TRUE)
    spList$genus <- gsub("(^[[:alpha:]])", "\\U\\1", spList$genus, perl = TRUE)
    spList$family <- gsub("(^[[:alpha:]])", "\\U\\1", spList$family, perl = TRUE)
    rnN <- data.frame(node.label = paste("N", 1:length(tree$node.label), sep = ""), oriN = tree$node.label, stringsAsFactors = FALSE)
    nodes[,c("level","family","genus","rn","bn","taxa")]<-lapply(nodes[,c("level","family","genus","rn","bn","taxa")], as.character)
    tree$node.label <- paste("N", 1:length(tree$node.label), sep = "")
    kk<-c()
    for (i in 1:length(tree$tip.label)) {
    kk<-c(kk,substring(tree$tip.label[i],1,gregexpr("_",tree$tip.label[i])[[1]][1]-1))
    }
    m<-data.frame(num=1:length(kk),genus=kk,species=tree$tip.label)
    m<-merge(m,nodes[,c("genus","family")])
    mX <- m
    m <- m[,c("genus","family")]
    m <- m[!duplicated(m$genus),]
    dimnames(m)[[2]][2] <- "family_in_PhytoPhylo"
    m<-m[,c("genus","family_in_PhytoPhylo")]
    m0 <- spList[!duplicated(spList$genus), c("genus","family")]
    dimnames(m0)[[2]][2] <- "family_in_spList"
    mm<-merge(m0, m)
    g<-mm[which(is.na(match(paste(mm$genus,mm$family_in_spList,sep="_"),paste(mm$genus,mm$family_in_PhytoPhylo,sep="_")))),]
    if (dim(g)[1]>0)
      {
        print("Taxonomic classification not consistent between spList and PhytoPhylo.")
        print(g) 
      }
    add.tip <- spList[which(is.na(match(spList$species, tree$tip.label))), ]
    status <- rep("match(prune)", dim(spList)[1])
    status[which(is.na(match(spList$species, tree$tip.label)))] <- "match(add)"
    if (dim(add.tip)[1] == 0 & length(na.omit(match(spList$species, tree$tip.label))) == 0)
        stop("Incorrect format of species list.")
    if (length(setdiff(spList$species, tree0$tip.label)) == 0 & length(na.omit(match(spList$species, tree$tip.label))) > 0)
     {
        print("There is no species needs to be added, all the species are pruned from PhytoPhylo.")
        splis <- spList.original
        treeX <- drop.tip(tree0, setdiff(tree0$tip.label, splis$species))
        splis$status <- "match(prune)"
        phylo0 <- list(Scenario.1 = NULL, Scenario.2 = NULL, Scenario.3 = NULL, Species.list = splis)
        if ("S1" %in% scenarios) {phylo0$Scenario.1 <- treeX}
        if ("S2" %in% scenarios) {phylo0$Scenario.2 <- treeX}
        if ("S3" %in% scenarios) {phylo0$Scenario.3 <- treeX}
        phylo0[sapply(phylo0, is.null)] <- NULL
        return(phylo0)
        stop()
     }
    add.tip$sort <- ""
    add.tip$sort[which(!is.na(match(add.tip$genus, nodes[nodes$level == "G", ]$genus)))] <- "G1"
    add.tip$sort[which(is.na(match(add.tip$genus, nodes[nodes$level == "G", ]$genus)) & !is.na(match(add.tip$family, nodes[nodes$level == "F", ]$family)))] <- "F1"
    add.tip$sort[add.tip$sort == "F1"][duplicated(add.tip[add.tip$sort == "F1", ]$genus)] <- "F2"
    a <- which(add.tip$sort == "")
    if (length(a) > 0)
      {  
        print(paste("Note:", length(a), "taxa unmatch:",sep=" "))
        print(add.tip$species[a])
        status[match(add.tip$species[a], spList$species)] <- "unmatch"         
      }  
    spList.original$status <- status
    if ("S1" %in% scenarios) {
        t1 <- tree
        rnN1<-rnN
        nG <- nodes[nodes$level == "G", ]
        nF <- nodes[nodes$level == "F", ]
        data <- add.tip[add.tip$sort == "F1", ]
       if (dim(data)[1] > 0) {
            for (i in 1:dim(data)[1]) {
                n <- match(data$family[i], nF$family)
                g <- nF$gen.n[n]
                s <- nF$sp.n[n]
                if (g == 1 & s == 1) {                                                                          
                  num <- grep(nF$taxa[n], t1$tip.label)
                  len <- t1$edge.length[match(num, t1$edge[, 2])]
                  t1 <- bind.tip(t1, tip.label = data$species[i], edge.length = len, where = num, position = len)
                  nF$gen.n[n] <- g + 1
                  nF$sp.n[n] <- s + 1
                  num <- grep(nF$taxa[n], t1$tip.label)
                  t1$node.label[match(t1$edge[match(num, t1$edge[, 2]), 1], unique(t1$edge[, 1]))] <- paste("NN", t1$Nnode + 1, sep = "")
                  rnN1$node.label[match(nF$bn[n], rnN1$node.label)]<- paste("NN", t1$Nnode + 1, sep = "")
                  nF$bn[n] <- paste("NN", t1$Nnode + 1, sep = "")
                  nF$bn.bl[n] <- len
                }             
                else {
                  num <- unique(t1$edge[, 1])[match(nF$bn[n], t1$node.label)]
                  len <- nF$bn.bl[n]
                  t1 <- bind.tip(t1, tip.label = data$species[i], edge.length = len, where = num)
                }
            }
        }
        data <- add.tip[add.tip$sort != "F1", ]
       if (dim(data)[1] > 0) {
            for (i in 1:dim(data)[1]) {
                n <- grep(paste(data$genus[i], "_", sep = ""), t1$tip.label)
              if (length(n) == 1) {
                  num <- n
                  len <- t1$edge.length[match(num, t1$edge[, 2])]
                  t1 <- bind.tip(t1, tip.label = data$species[i], edge.length = len, where = num, position = len)
                  }
              if (length(n) > 1) {
                  num <- fastMRCA(t1, t1$tip.label[min(n)], t1$tip.label[max(n)])
                  len <- fastDist(t1, t1$tip.label[min(n)], t1$tip.label[max(n)])/2
                  t1 <- bind.tip(t1, tip.label = data$species[i], edge.length = len, where = num)
                  }   
               }
            }
        toDrop <- setdiff(1:length(t1$tip.label), which(!is.na(match(t1$tip.label, spList$species))))
        t1 <- drop.tip(t1, tip = toDrop)
        Re <- which(!is.na(match(t1$node.label, rnN1$node.label)))
        noRe <- which(is.na(match(t1$node.label, rnN1$node.label)))
        t1$node.label[Re] <- rnN1$oriN[match(t1$node.label, rnN1$node.label)[Re]]
        t1$node.label[noRe] <- ""
    }
    else {
        t1 <- NULL
    }
    if ("S2" %in% scenarios) {
        t2 <- tree
        rnN2<-rnN
        nG <- nodes[nodes$level == "G", ]
        nF <- nodes[nodes$level == "F", ]
        data <- add.tip[add.tip$sort == "F1", ]
        if (dim(data)[1] > 0) {
            for (i in 1:dim(data)[1]) {
                n <- match(data$family[i], nF$family)
                g <- nF$gen.n[n]
                s <- nF$sp.n[n]
                if (g == 1 & s == 1) {
                  num <- grep(nF$taxa[n], t2$tip.label)
                  len <- t2$edge.length[match(num, t2$edge[,2])] * sample((1:99)/100,1)
                  t2 <- bind.tip(t2, tip.label = data$species[i], edge.length = len, where = num, position = len)    
                  nF$gen.n[n] <- g + 1
                  nF$sp.n[n] <- s + 1
                  num <- grep(data$species[i], t2$tip.label)
                  t2$node.label[match(t2$edge[match(num, t2$edge[, 2]), 1], unique(t2$edge[,1]))] <- paste("NN", t2$Nnode + 1, sep = "")
                  rnN2$node.label[match(nF$bn[n], rnN2$node.label)]<- paste("NN", t2$Nnode + 1, sep = "")
                  nF$bn[n] <- paste("NN", t2$Nnode + 1, sep = "")
                  nF$bn.bl[n] <- len
                }
                else {
                  num <- unique(t2$edge[, 1])[match(nF$bn[n], t2$node.label)]
                  len <- t2$edge.length[match(num,t2$edge[,2])] * sample((1:99)/100,1)
                  t2 <- bind.tip(t2, tip.label = data$species[i], edge.length = len, where = num, position = len)
                  nF$gen.n[n] <- g + 1
                  nF$sp.n[n] <- s + 1
                  num <- grep(data$species[i], t2$tip.label)
                  t2$node.label[match(t2$edge[match(num, t2$edge[, 2]), 1], unique(t2$edge[, 1]))] <- paste("NN", t2$Nnode + 1, sep = "")
                  rnN2$node.label[match(nF$bn[n], rnN2$node.label)]<- paste("NN", t2$Nnode + 1, sep = "")
                  nF$bn[n] <- paste("NN", t2$Nnode + 1, sep = "")
                  nF$bn.bl[n] <- nF$bn.bl[n]+len
                }
            }
        }
       data <- add.tip[add.tip$sort != "F1", ]
       if (dim(data)[1] > 0) {
            for (i in 1:dim(data)[1]) {
                n <- grep(paste(data$genus[i], "_", sep = ""), t2$tip.label)
              if (length(n) == 1) {
                  num <- n
                  len <- t2$edge.length[match(num, t2$edge[, 2])] * sample((1:99)/100,1)
                  t2 <- bind.tip(t2, tip.label = data$species[i], edge.length = len, where = num, position = len)
                  }
              if (length(n) > 1) {
                  num <- sample(n,1)
                  len <- t2$edge.length[match(num, t2$edge[, 2])] * sample((1:99)/100,1)
                  t2 <- bind.tip(t2, tip.label = data$species[i], edge.length = len, where = num, position = len)
                  }   
               }
         }
        toDrop <- setdiff(1:length(t2$tip.label), which(!is.na(match(t2$tip.label, spList$species))))
        t2 <- drop.tip(t2, tip = toDrop)
        Re <- which(!is.na(match(t2$node.label, rnN2$node.label)))
        noRe <- which(is.na(match(t2$node.label, rnN2$node.label)))
        t2$node.label[Re] <- rnN2$oriN[match(t2$node.label, rnN2$node.label)[Re]]
        t2$node.label[noRe] <- ""
    }
    else {
        t2 <- NULL
    }
          if ("S3" %in% scenarios) {
        t3 <- tree
        rnN3<-rnN
        nG <- nodes[nodes$level == "G", ]
        nF <- nodes[nodes$level == "F", ]
        data <- add.tip[add.tip$sort == "F1", ]
        if (dim(data)[1] > 0) {
            for (i in 1:dim(data)[1]) {
                n <- match(data$family[i], nF$family)
                g <- nF$gen.n[n]
                s <- nF$sp.n[n]
                if (g == 1 & s == 1) {                                                                          
                  num <- grep(nF$taxa[n], t3$tip.label)
                  len <- t3$edge.length[match(num, t3$edge[, 2])] * (2/3)
                  t3 <- bind.tip(t3, tip.label = data$species[i], edge.length = len, where = num, position = len)
                  nF$gen.n[n] <- g + 1
                  nF$sp.n[n] <- s + 1


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> 3、现在给你三百台服务器，你怎么对他们进行管理?

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> 5、LVS、Nginx、HAproxy有什么区别?工作中你怎么选择?

> 6、Squid、Varinsh和Nginx有什么区别，工作中你怎么选择?

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> 12、简述DNS进行域名解析的过程?

> 13、RabbitMQ是什么东西?

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