Package: ape
-Version: 2.7-2
-Date: 2011-06-01
+Version: 2.7-3
+Date: 2011-06-14
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Klaus Schliep, Korbinian Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
+ CHANGES IN APE VERSION 2.7-3
+
+
+NEW FEATURES
+
+ o There is a new predict() method for compar.gee().
+
+
+
CHANGES IN APE VERSION 2.7-2
NEW FEATURES
- o plot.phylo() has a new option 'draw = TRUE'. If FALSE, the tree
+ o There is a new class "evonet" to code evolutionary networks, with
+ a constructor function evonet(), a print() and a plot() methods,
+ and four conversion methods to the classes "phylo", "networx",
+ "network", and "igraph".
+
+ o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
is not plotted but the graphical device is set and the
coordinates are saved as usual.
o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
the aspect of the bar.
+ o boot.phylo() now displays a progress bar by default (can be off
+ if 'quiet = TRUE').
+
BUG FIXES
o read.nexus.data() failed with URLs.
+ o boot.phylo() returned overestimated support values in the
+ presence of identical or nearly identical sequences.
+
CHANGES IN APE VERSION 2.7-1
-## compar.gee.R (2010-07-20)
+## compar.gee.R (2011-06-14)
## Comparative Analysis with GEEs
QIC = QIC,
coefficients = geemod$coefficients,
residuals = geemod$residuals,
+ fitted.values = MU,
family = geemod$family$family,
link = geemod$family$link,
scale = geemod$scale,
as.character(as.expression(fm)), "\n")
ans
}
+
+predict.compar.gee <-
+ function(object, type = c("link", "response"), ...)
+{
+ type <- match.arg(type)
+ pred <- object$fitted.values
+ if (type == "link") return(pred)
+ f <- match.fun(object$family)
+ f(link = object$link)$linkinv(pred)
+}
-## dist.topo.R (2011-03-26)
+## dist.topo.R (2011-06-14)
## Topological Distances, Tree Bipartitions,
## Consensus Trees, and Bootstrapping Phylogenies
n
}
-boot.phylo <- function(phy, x, FUN, B = 100, block = 1, trees = FALSE)
+boot.phylo <- function(phy, x, FUN, B = 100, block = 1,
+ trees = FALSE, quiet = FALSE)
{
if (is.list(x) && !is.data.frame(x)) {
if (inherits(x, "DNAbin")) x <- as.matrix(x)
}
}
boot.tree <- vector("list", B)
+ if (!quiet) progbar <- utils::txtProgressBar(style = 3) # suggestion by Alastair Potts
for (i in 1:B) {
if (block > 1) {
y <- seq(block, ncol(x), block)
boot.samp[y - j] <- boot.i - j
} else boot.samp <- sample(ncol(x), replace = TRUE)
boot.tree[[i]] <- FUN(x[, boot.samp])
+ if (!quiet) utils::setTxtProgressBar(progbar, i/B)
}
+ if (!quiet) close(progbar)
for (i in 1:B) storage.mode(boot.tree[[i]]$Nnode) <- "integer"
storage.mode(phy$Nnode) <- "integer"
- ans <- attr(.Call("prop_part", c(list(phy), boot.tree),
- B + 1, FALSE, PACKAGE = "ape"), "number") - 1
+ ans <- prop.clades(phy, boot.tree)
+ ##ans <- attr(.Call("prop_part", c(list(phy), boot.tree),
+ ## B + 1, FALSE, PACKAGE = "ape"), "number") - 1
if (trees) {
class(boot.tree) <- "multiPhylo"
ans <- list(BP = ans, trees = boot.tree)
cat(" log-likelihood =", round(loglik.B, 3),
" AIC =", round(-2 * loglik.B + 4, 3), "\n")
cat(" alpha =", round(alpha, 6), " StdErr =", round(sqrt(var.alpha), 6), "\n")
- cat(" beta =", round(beta, 6), " StdErr =", round(sqrt(var.beta), 6), "\n\n")
+ cat(" beta =", round(beta, 6), " StdErr =", round(sqrt(var.beta), 6), "\n\n")
cat("Model C: diversification changes with a breakpoint at time =", Tc, "\n")
cat(" log-likelihood =", round(loglik.C, 3),
" AIC =", round(-2 * loglik.C + 4, 3), "\n")
--- /dev/null
+## evonet.R (2011-06-09)
+
+## Evolutionary Networks
+
+## Copyright 2011 Emmanuel Paradis
+
+## This file is part of the R-package `ape'.
+## See the file ../COPYING for licensing issues.
+
+evonet <- function(phy, from, to = NULL)
+{
+ if (!inherits(phy, "phylo"))
+ stop('object "phy" is not of class "phylo".')
+ if (!is.rooted(phy))
+ warning("the tree is unrooted")
+ x <- phy
+
+ if (is.null(to)) {
+ if (is.data.frame(from))
+ from <- as.matrix(from)
+ if (!is.matrix(from))
+ stop("'from' must be a matrix or a data frame if 'to' is not given")
+ if (ncol(from) > 2) {
+ warning("'from' has more than two columns: only the first two will be used.")
+ ret <- from[, 1:2]
+ } else if (ncol(from) < 2) {
+ stop("'from' must have at least two columns")
+ } else ret <- from
+ } else {
+ from <- as.vector(from)
+ to <- as.vector(to)
+ if (length(from) != length(to))
+ stop("'from' and 'to' not of the same length after coercing as vectors")
+ ret <- cbind(from, to)
+ }
+
+ ## check that values are not out of range:
+ storage.mode(ret) <- "integer"
+ if (any(is.na(ret)))
+ stop("some values are NA's after coercing as integers")
+ if (any(ret < 0) || any(ret > Ntip(phy) + phy$Nnode))
+ stop("some values are out of range")
+
+ x$reticulation <- ret
+ class(x) <- c("evonet", "phylo")
+ x
+}
+
+as.phylo.evonet <- function(x, ...)
+{
+ x$reticulation <- NULL
+ class(x) <- "phylo"
+ x
+}
+
+plot.evonet <- function(x, col = "blue", lty = 1, lwd = 1, alpha = 0.5,
+ arrows = 0, arrow.type = "classical", ...)
+{
+ plot.phylo(as.phylo(x), ...)
+ ape::edges(x$reticulation[, 1], x$reticulation[, 2],
+ col = rgb(t(col2rgb(col)), alpha = 255 * alpha,
+ maxColorValue = 255), lty = lty, lwd = lwd,
+ arrows = arrows, type = arrow.type)
+}
+
+as.networx.evonet <- function(x, weight = NA, ...)
+{
+ if (any(x$reticulation <= Ntip(x)))
+ stop("some tips are involved in reticulations: cannot convert to \"networx\"")
+ x <- reorder(x, "p")
+ ned <- Nedge(x)
+ nrt <- nrow(x$reticulation)
+ x$edge <- rbind(x$edge, x$reticulation)
+ colnames(x$edge) <- c("oldNodes", "newNodes")
+ x$reticulation <- NULL
+ x$edge.length <- c(x$edge.length, rep(weight, length.out = nrt))
+ x$split <- c(1:ned, 1:nrt)
+ class(x) <- c("networx", "phylo")
+ x
+}
+
+as.network.evonet <- function(x, directed = TRUE, ...)
+{
+ class(x) <- NULL
+ x$edge <- rbind(x$edge, x$reticulation)
+ as.network.phylo(x, directed = directed, ...)
+}
+
+as.igraph.evonet <- function(x, directed = TRUE, use.labels = TRUE, ...)
+{
+ class(x) <- NULL
+ x$edge <- rbind(x$edge, x$reticulation)
+ as.igraph.phylo(x, directed = directed, use.labels = use.labels, ...)
+}
+
+print.evonet <- function(x, ...)
+{
+ nr <- nrow(x$reticulation)
+ cat("\n Evolutionary network with", nr, "reticulation")
+ if (nr > 1) cat("s")
+ cat("\n\n --- Base tree ---")
+ print.phylo(as.phylo(x))
+}
-## plot.phylo.R (2011-03-29)
+## plot.phylo.R (2011-06-14)
## Plot Phylogenies
adj = NULL, srt = 0, no.margin = FALSE, root.edge = FALSE,
label.offset = 0, underscore = FALSE, x.lim = NULL,
y.lim = NULL, direction = "rightwards", lab4ut = "horizontal",
- tip.color = "black", draw = TRUE, ...)
+ tip.color = "black", plot = TRUE, ...)
{
Ntip <- length(x$tip.label)
if (Ntip == 1) {
asp <- if (type %in% c("fan", "radial", "unrooted")) 1 else NA # fixes by Klaus Schliep (2008-03-28 and 2010-08-12)
plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE, axes = FALSE, asp = asp, ...)
-if (draw) {
+if (plot) {
if (is.null(adj))
adj <- if (phyloORclado && direction == "leftwards") 1 else 0
if (phyloORclado && show.tip.label) {
}
x
}
+
+rTraitMult <-
+ function(phy, model, p = 1, root.value = rep(0, p), ancestor = FALSE,
+ as.factor = NULL, ...)
+{
+ phy <- reorder(phy, "pruningwise")
+ n <- length(phy$tip.label)
+ m <- phy$Nnode
+ N <- dim(phy$edge)[1]
+ ROOT <- n + 1L
+
+ x <- matrix(0, n + m, p)
+ x[ROOT, ] <- root.value
+
+ anc <- phy$edge[, 1]
+ des <- phy$edge[, 2]
+
+ el <- phy$edge.length
+ if (is.null(el)) el <- numeric(N)
+
+ for (i in N:1) x[des[i], ] <- model(x[anc[i], ], el[i], ...)
+
+ if (ancestor) {
+ if (is.null(phy$node.label)) phy <- makeNodeLabel(phy)
+ rownames(x) <- c(phy$tip.label, phy$node.label)
+ } else {
+ x <- x[1:n, , drop = FALSE]
+ rownames(x) <- phy$tip.label
+ }
+ x <- as.data.frame(x)
+ if (!is.null(as.factor)) {
+ for (i in as.factor) {
+ y <- x[, i]
+ x[, i] <- factor(y, labels = LETTERS[1:length(unique(y))])
+ }
+ }
+ x
+}
### ROTATE
-### Last update CH on 09.08.2007
+### Last update CH on 09.08.2007 (updated by EP 2011-06-14)
# Contents:
# 1. rotate
phy$edge.length <- c(phy$edge.length[c3:c4], phy$edge.length[(c2+1):(c3-1)], phy$edge.length[c1:c2])
}
}
- S <- write.tree(phy)
- phy <- if (!with.br.length) clado.build(S) else tree.build(S)
+ ## deleted by EP (2011-06-14):
+ ## S <- write.tree(phy)
+ ## phy <- if (!with.br.length) clado.build(S) else tree.build(S)
phy
}
+++ /dev/null
-require(ape, quietly = TRUE)
-bird.families <- read.tree("bird.families.tre")
+++ /dev/null
-(((((Struthionidae:17.1,Rheidae:17.1):0.8,
-(Casuariidae:9.5,Apterygidae:9.5):8.4):3.9,Tinamidae:21.8):4.1,
-(((Cracidae:19.8,Megapodiidae:19.8):1.8,
-((Phasianidae:12.8,Numididae:12.8):2.3,Odontophoridae:15.1):6.5):1.3,
-((Anhimidae:12.4,Anseranatidae:12.4):3.7,
-(Dendrocygnidae:9.8,Anatidae:9.8):6.3):6.8):3.0):2.1,
-(Turnicidae:27.0,(((Indicatoridae:11.0,Picidae:11.0):5.5,
-(Megalaimidae:12.8,(Lybiidae:11.5,Ramphastidae:11.5):1.3):3.7):9.8,
-(((Galbulidae: 17.5,Bucconidae: 17.5):6.9,
-(((Bucerotidae:9.2,Bucorvidae:9.2):11.6,
-(Upupidae:17.0,(Phoeniculidae:10.2,Rhinopomastidae:10.2):6.8):3.8):2.6,
-(Trogonidae:22.1,((Coraciidae:13.9,Leptosomidae:13.9):7.1,
-(Meropidae:19.7,(Momotidae:17.7,(Todidae:16.5,(Alcedinidae:15.5,
-(Dacelonidae:12.0,Cerylidae:12.0):3.5):1.0):1.2):2.0):1.3):1.1):1.3):1.0):0.6,
-(Coliidae:24.5,
-((((Cuculidae:13.0,Centropidae:13.0):1.5,Coccyzidae:14.5):3.1,
-(Opisthocomidae:16.4,(Crotophagidae:14.5,Neomorphidae:14.5):1.9):1.2):6.1,
-(Psittacidae:23.1,
-((((Apodidae:9.5,Hemiprocnidae:9.5):11.8,Trochilidae:21.3):0.6,
-(Musophagidae:20.4,((Tytonidae:13.6,Strigidae:13.6):5.5,
-(Aegothelidae:18.8,((Podargidae:10.3,Batrachostomidae:10.3):7.6,
-((Steatornithidae:15.8,Nyctibiidae:15.8):1.1,
-(Eurostopodidae:12.3,Caprimulgidae:12.3):4.6):1.0):0.9):0.3):1.3):1.5):0.6,
-((Columbidae:20.8,(((Eurypygidae:17.5,
-(Otididae:16.9,(((Gruidae:9.2,Heliornithidae:9.2):3.5,
-Psophiidae:12.7):2.3,Cariamidae:15.0,Rhynochetidae:15.0):1.9):0.6):1.6,Rallidae:19.1):1.0,
-((Pteroclidae:17.1,
-((((Thinocoridae:10.3,Pedionomidae:10.3):3.0,Scolopacidae:13.3):0.8,
-(Rostratulidae:12.5,Jacanidae:12.5):1.6):1.5,
-((Chionididae:11.5,(Burhinidae:10.8,Charadriidae:10.8):0.7):1.3,
-(Glareolidae:8.1,Laridae:8.1):4.7):2.8):1.5):1.6,
-(((Accipitridae:10.4,Sagittariidae:10.4):4.8,Falconidae:15.2):1.2,
-(Podicipedidae:14.9,(Phaethontidae:14.0,
-(((Sulidae:11.0,Anhingidae:11.0):1.1,Phalacrocoracidae:12.1):1.2,
-(Ardeidae:12.4,(Scopidae:11.9,
-(Phoenicopteridae:11.5,(Threskiornithidae:11.1,
-((Pelecanidae:10.1,Ciconiidae:10.1):0.8,
-(Fregatidae:10.7,(Spheniscidae:10.4,(Gaviidae:10.0,
-Procellariidae:10.0):0.4):0.3):0.2):0.2):0.4):0.4):0.5):0.9):0.7):0.9):1.5):2.3):1.4):0.7):0.8,
-((Acanthisittidae:17.9,((Pittidae:12.1,Eurylaimidae:12.1):3.7,
-(Tyrannidae:13.8,(Thamnophilidae:13.5,(Furnariidae:12.1,(Formicariidae:11.4,
-(Conopophagidae:10.7,Rhinocryptidae:10.7):0.7):0.7):1.4):0.3):2.0):2.1):1.8,
-(((Climacteridae:10.4,(Menuridae:9.9,Ptilonorhynchidae:9.9):0.5):1.3,
-((Maluridae:11.2,(Meliphagidae:9.2,Pardalotidae:9.2):2.0):0.2,
-(Eopsaltriidae:10.6,(Irenidae:10.2,(Orthonychidae:10.0,(Pomatostomidae:9.6,
-(Laniidae:9.1,(Vireonidae:8.8,Corvidae:8.8):0.3):0.5):0.4):0.2):0.4):0.8):0.3):1.1,
-((Bombycillidae:10.6,(Cinclidae:9.7,(Muscicapidae:9.1,Sturnidae:9.1):0.6):0.9):1.1,
-(((Sittidae:10.0,Certhiidae:10.0):0.8,
-(Paridae:10.6,(Aegithalidae:10.4,(Hirundinidae:10.1,
-(Regulidae:9.7,(Pycnonotidae:9.5,(Cisticolidae:9.4,
-(Zosteropidae:9.1,Sylviidae:9.1):0.3):0.1):0.2):0.4):0.3):0.2):0.2):0.3,
-(Alaudidae:10.4,(((Nectariniidae:9.6,
-(Melanocharitidae:9.3,Paramythiidae:9.3):0.3):0.2,
-Passeridae:9.8):0.2,Fringillidae:10.0):0.4):0.7):0.6):1.1):6.9):1.9):0.9):0.6):0.6):0.8):0.5):1.3):0.7):1.0);
+++ /dev/null
-require(ape, quietly = TRUE)
-bird.orders <- read.tree("bird.orders.tre")
+++ /dev/null
-(((Struthioniformes:21.8,Tinamiformes:21.8):4.1,
-((Craciformes:21.6,Galliformes:21.6):1.3,Anseriformes:22.9):3.0):2.1,
-(Turniciformes:27.0,(Piciformes:26.3,((Galbuliformes:24.4,
-((Bucerotiformes:20.8,Upupiformes:20.8):2.6,
-(Trogoniformes:22.1,Coraciiformes:22.1):1.3):1.0):0.6,
-(Coliiformes:24.5,(Cuculiformes:23.7,(Psittaciformes:23.1,
-(((Apodiformes:21.3,Trochiliformes:21.3):0.6,
-(Musophagiformes:20.4,Strigiformes:20.4):1.5):0.6,
-((Columbiformes:20.8,(Gruiformes:20.1,Ciconiiformes:20.1):0.7):0.8,
-Passeriformes:21.6):0.9):0.6):0.6):0.8):0.5):1.3):0.7):1.0);
+++ /dev/null
-require(ape, quietly = TRUE)
-cynipids <- read.nexus.data("cynipids.txt")
-
+++ /dev/null
-#NEXUS
-[LWRh data from Rokas et al. 2002. Molecular Phylogenetics and Evolution 22:206-219]
-BEGIN DATA;
- DIMENSIONS NTAX=8 NCHAR=159;
- FORMAT MISSING=? GAP=- DATATYPE=PROTEIN INTERLEAVE=YES;
- MATRIX
- Barbotinia_oraniensis LGPFICEIYAMLGSLFGCGSIWTMCMIAFDRYNVIVKGLAGKPLTISGAI
- Synergus_gallaepomiformis LGPFICEMYGMFGSLFGCGSIWTMCMIAFDRYNVIVKGLVGKPLTISGAI
- Periclistus_brandtii LGPFMCEIYAMLGSLFGCGSIWTMCMIAFDRYNVIVKGLAGKPLSISGAI
- Panteliella_bicolor LGPFLCEMYGMFGSLFGCGSIWTMCMIAFDRYNVIVKGLAGKPLTITGAI
- Plagiotrochus_quercusilicis HGPFMCEMYAMFGSLFGCGSIWTMCMIAFDRYNVIVKGLAGKPLTISGAI
- Andricus_curvator LGPFMCEIYAMLGSLFGCGSIWTMCMIAFDRYNVIVKGLAGKPLTISGAI
- Andricus_kollari LGPFMCEIYAMLGSLFGCVSIWTMCMIAFDRYNVIVKGLAGKPLTISGAI
- Diplolepis_rosae -GPFLCEIYALLGSLFGCGSIWTMCMIAFDRYNVIVKGLAGKPLTITGAI
-
- Barbotinia_oraniensis LRIVFLWVWAVVWTIAPMIGWNRYVPEGNMTACGTDYLTKDWFSRSYILV
- Synergus_gallaepomiformis LRIAFLWIWAVIWTIAPMIGWNRYVPEGNMTACGTDYLSKDWFSRSYIIV
- Periclistus_brandtii LRIVGLWVWAVIWTIAPMIGWNRYVPEGNLTACGTDYLSKDWLSRSYILV
- Panteliella_bicolor LRIVGLWVWAVIWTIAPMIGWNRYVPEGNMTACGTDYLNKDWFSRSYILI
- Plagiotrochus_quercusilicis LRIVGLWVWAVIWTIAPMLGWNRYVPEGNMTACGTDYLTKDWFSRSYILV
- Andricus_curvator LRIVGLWVWAVIWTIAPMLGWNRYVPEGNMTACGTDYLSKDWFSRSYILV
- Andricus_kollari LRIVGLWVWAIIWTIAPMLGWNRYVPEGNMTACGTDYLSKDWFSRSYIIV
- Diplolepis_rosae IRIIGLWVWAIIWTIAPMFGWNRYVPEGNMTACGTDYLSKDWFSRSYILV
-
- Barbotinia_oraniensis YSVFVYFMPLFLIIYSYYFIIAAVSAHEKAMREQAKKMNVASLRSSDNQN
- Synergus_gallaepomiformis YSVFVYFMPLFLIIYSYYFIIAAVSAHEKAMREQAKKMNVASLRSSDNQN
- Periclistus_brandtii YSVFVYFMPLFLIIYSYYFIIAAVSAHEKAMREQAKKMNVASLRSSDNQN
- Panteliella_bicolor YSVFVYFMPLFLIIYSYYFIIAAVSAHEKAMREQAKKMNVASLRSSDNQN
- Plagiotrochus_quercusilicis YSVFVYFMPLFLIIYSYYFIIAAVTAHEKAMREQAKKMNVASLRSSDNQN
- Andricus_curvator YSIFVYFMPLFLIIYSYYFIIAAVTAHEKAMREQAKKMNVASLRSSDNQN
- Andricus_kollari YSIFVYFMPLFLIIYSYYFIIAAVTAHEKAMREQAKKMNVASLRSSDNQN
- Diplolepis_rosae YSIFVYYMPLFLIIYSYYFIISAVSAHEKAMREQAKKMNVASLRSSDNAN
-
- Barbotinia_oraniensis TSAEHKLAK
- Synergus_gallaepomiformis TSAEHKLAK
- Periclistus_brandtii TSAEHKLAK
- Panteliella_bicolor TSAEHKLAK
- Plagiotrochus_quercusilicis TSAEHKLAK
- Andricus_curvator TSAEHKLAK
- Andricus_kollari TSAEHKLAK
- Diplolepis_rosae TSAEHKLAK
- ;
-END;
-
+++ /dev/null
-require(ape, quietly = TRUE)
-woodmouse <- read.dna("woodmouse.txt", format = "sequential")
+++ /dev/null
-15 965
-No305 NTTCGAAAAACACACCCACTACTAAAANTTATCAGTCACTCCTTCATCGACTTACCAGCTCCATCTAACATTTCATCATGATGAAACTTCGGCTCATTACTAGGAGTCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGTCGAGACGTAAATTATGGCTGACTAATTCGATACATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATGTATTACGGGTCATACATTTTCATAGAAACATGAAACATCGGTGTGGTCCTTTTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAANTTACTATCAGCAATTCCATACATCGGAACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCCACACTGACACGTTTTTTCGCTTTTCACTTTATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTCCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGTGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATATTTCCTATTTGCCTATGCAATCCTACGATCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAGACCCTATA
-No304 ATTCGAAAAACACACCCACTACTAAAAATTATCAACCACTCCTTCATCGACTTACCAGCTCCATCTAACATTTCATCATGATGAAACTTCGGCTCATTACTAGGAATCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGTCGAGACGTAAATTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATGTATTACGGGTCATACATTTTTATAGAAACATGAAACATCGGTGTAGTCCTTTTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTNCAAATTTACTNTCAGCAATTCCATACATCGGAACTACCCTAGTAGAATGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTCATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGTGTACTAATAATAGTTTCCTTCCTAATAACTCTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATACTTCCTATTTGCCTATGCAATCCTACGGTCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCTGTN
-No306 ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACTCCTTCATCGACTTACCAGCTCCATCTAACATTTCATCATGATGAAACTTCGGCTCATTACTAGGAATCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGTCGAGACGTAAATTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATGTATTACGGGTCATACATTTTTATAGAAACATGAAACATCGGTGTGATCCTTTTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAATTTACTATCAGCAATTCCATACATCGGAACTACCCTAGTAGAATGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTCATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGTGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACNNCATATTAAACCAGAATGATACTTCCTATTTGCCTATGCAATCCTACGGTCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCTATA
-No0906S ATTCGAAAAACACACCCACTACTAAAAATCATCAATCACTCCTTCATCGATTTACCAGCTCCATCTAACATTTCATCATGATGAAACTTCGGCTCATTACTAGGAATCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGTCGAGACGTAAATTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATGTATTACGGATCATACATTTTTATAGAAACATGAAACATCGGTATGATCCTTTTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAATTTACTATCAGCAATTCCATACATCGGAACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTCATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGTGTACTAATAATAATTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATACTTCCTATTTGCCTATGCAATCCTACGATCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAATACNNNN
-No0908S ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACTCCTTCATCGACTTACCAGCCCCATCTAACATTTCATCATGATGAAACTTCGGCTCATTACTAGGAATCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGTCGAGACGTAAATTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTCCATGTAGGACGAGGAATGTATTACGGGTCATACATTTTTATAGAAACATGAAACATCGGTGTGATCCTTTTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGGGCTACAGTAATTACAAATTTACTATCAGCAATTCCATATATCGGAACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTCATCCTCCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGTGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATACTTCCTATTTGCCTATGCAATCCTACGATCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCNNNN
-No0909S ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACTCCTTCATCGACTTACCAGCTCCATCTAACATCTCATCATGATGAAACTTCGGCTCCTTACTAGGAATCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGTCGAGACGTAAACTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATGTATTACGGGTCATACACTTTCATAGAAACATGAAACATCGGTGTGATCCTTCTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAATTTACTATCAGCAATTCCATACATCGGGACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTTATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGTGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATACTTCCTATTTGCCTATGCAATCCTACGATCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATCCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCNNNN
-No0910S ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACTCTTTCATCGATTTACCAGCTCCATCTAACATTTCATCATGATGAAACTTCGGCTCATTACTAGGAATCTGCCTAATAATCCAGATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGTCGAGACGTAAATTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATGTATTACGGATCATACATTTTTATAGAAACATGAAACATCGGTGTGATCCTTTTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAATTTACTATCAGCAATTCCATACATCGGAACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTCATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGCGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATACTTCCTATTTGCCTATGCAATCCTACGATCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTGCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCNNNN
-No0912S ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACTCCTTCATCGACTTACCAGCTCCATCTAACATCTCATCATGATGAAACTTCGGCTCCTTACTAGGAATCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGTCGAGACGTAAATTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGGGGAATGTATTACGGGTCATACATTTTCATAGAAACATGAAACATCGGTGTGATCCTTTTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAATTTACTATCAGCAATTCCATACATCGGAACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTCCACTTCATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGACATTCTAGGTGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATATTTCCTATTTGCCTATGCAATCCTACGATCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCNNNN
-No0913S ATTCGAAAAACACACCCACTACTAAAAATTATCAACCACTCCTTCATCGACTTACCAGCTCCATCTAACATTTCATCATGATGAAACTTCGGCTCATTACTAGGAATCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGTCGAGACGTAAATTATGGCTGACTAATTCGATATATGCATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATGTATTACGGATCATACATTTTTATAGAAACATGAAACATCGGTGTGATCCTTTTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAATTTACTATCAGCAATTCCATACATCGGAACTACCCTAGTAGAATGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTCATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGCGTACTAATAATAGTTTCCTTCCTAATAACTCTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATACTTCCTATTTGCCTATGCAATCCTACGGTCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCNNNN
-No1103S ATTCGAAAAACACACCCACTACTAAAAATTATTAATCACTCCTTCATCGACTTACCAGCTCCATCTAACATCTCATCATGATGAAACTTCGGCTCCTTACTAGGAATCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGTCGAGACGTAAATTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATGTATTACGGGTCATACATTTTCATAGAAACATGAAACATCGGTGTGATCCTTTTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAATTTACTATCAGCAATTCCATACATCGGAACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTCATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGTGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATATTTCCTATTTGCCTATGCAATCCTACGATCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCNNNN
-No1007S ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACTCCTTCATCGACTTACCAGCTCCATCTAACATCTCATCATGATGAAACTTCGGCTCCTTACTAGGAATCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGCCGAGACGTAAATTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATGTATTACGGGTCATACACTTTCATAGAAACATGAAACATCGGTGTGATCCTTCTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAATTTACTATCAGCAATTCCATACATCGGGACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTTATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGTGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATACTTCCTATTTGCCTATGCAATCCTACGATCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATCCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCNNNN
-No1114S NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATCGACTTACCAGCTCCATCTAACATTTCATCATGATGAAACTTCGGCTCATTACTAGGAGTCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGNAACCCATATTTGCCGAGACGTAAATTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATATATTACGGCTCATACATTCTCATAGAAACATGAAACATCGGTGTGGTCCTTTTATTCGCAGTAATAGTCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAATTTCCTATCAGCAATTCCATACATCGGAACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTTATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAGGATATTCTAGGTGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATATTTCCTATTTGCCTATGCAATCCTACGGTCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTCCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCNNNN
-No1202S ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACTCCTTCATCGATTTACCAGCTCCATCTAACATTTCATCATGATGAAACTTCGGCTCATTACTAGGAATCTGCCTAATAATCCAGATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGCCGAGACGTAAATTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATGTATTACGGATCATACATTTTTATAGAAACATGAAACATCGGTGTGATCCTTTTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAATTTACTATCAGCAATTCCATACATCGGAACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTCATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGCGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATACTTCCTATTTGCCTATGCAATCCTACGATCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCNNNN
-No1206S ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACTCCTTCATCGATTTGCCAGCTCCATCTAACATTTCATCATGATGAAACTTCGGCTCATTACTAGGAATCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGTCGAGACGTAAATTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTCCATGTAGGACGAGGAATGTATTACGGGTCATACATTTTTATAGAAACATGAAACATCGGTGTGATCCTTTTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCTTCTGAGGAGCTACAGTAATTACAAATTTACTATCAGCAATTCCATACATCGGAACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTCATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTGCACCTCTTGTTTCTTCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGTGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTCTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATACTTCCTATTTGCCTATGCAATCCTACGATCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATTCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCNNNN
-No1208S NNNCGAAAAACACACCCACTACTAAAAATTATCAATCACTCCTTCATCGACTTACCAGCTCCATCTAACATCTCATCATGATGAAACTTCGGCTCCTTACTAGGAATCTGCCTAATAATCCAAATCCTCACAGGCTTATTCCTAGCAATACACTACACATCAGACACAATAACAGCATTCTCTTCAGTAACCCATATTTGCCGAGACGTAAACTATGGCTGACTAATTCGATATATACATGCAAACGGAGCCTCAATATTTTTTATTTGCCTATTTCTTCATGTAGGACGAGGAATGTATTACGGGTCATACACTTTCATAGAAACATGAAACATCGGTGTGATCCTTCTATTCGCAGTAATAGCCACAGCATTCATAGGATATGTTCTTCCATGAGGACAAATATCCCTCTGAGGAGCTACAGTAATTACAAATTTACTATCAGCAATTCCATACATCGGGACTACCCTAGTAGAGTGAATCTGAGGAGGATTCTCAGTAGACAAAGCTACATTGACACGTTTTTTCGCTTTTCACTTTATCCTTCCATTTATCATTGCCGCCCTAGTAATTGTTCACCTCTTGTTTCTCCATGAAACTGGATCTAATAACCCAACAGGCCTTAACTCAGACGCCGATAAAATCCCATTTCACCCTTACTATACAATTAAAGATATTCTAGGTGTACTAATAATAGTTTCCTTCCTAATAACTTTAGTCCTTTTCTTTCCAGACCTTTTAGGTGACCCGGACAACTACATGCCTGCTAACCCACTTAACACCCCACCTCATATTAAACCAGAATGATACTTCCTATTTGCCTATGCAATCCTACGATCCATCCCCAATAAACTAGGCGGAGTCCTAGCCCTAATCCTATCAATCTTAATTTTAGCCTTATTACCATTTCTTCACACTTCCAAACAACGCAGCCTAATATTCCGCCCAATTACTCAAACCCNNNN
\ No newline at end of file
\alias{plot.prop.part}
\title{Tree Bipartition and Bootstrapping Phylogenies}
\usage{
-boot.phylo(phy, x, FUN, B = 100, block = 1, trees = FALSE)
+boot.phylo(phy, x, FUN, B = 100, block = 1,
+ trees = FALSE, quiet = FALSE)
prop.part(..., check.labels = TRUE)
prop.clades(phy, ..., part = NULL)
\method{print}{prop.part}(x, ...)
together (see details).}
\item{trees}{a logical specifying whether to return the bootstraped
trees (\code{FALSE} by default).}
+ \item{quiet}{a logical: a progress bar is displayed by default.}
\item{\dots}{either (i) a single object of class \code{"phylo"}, (ii) a
series of such objects separated by commas, or (iii) a list
containing such objects. In the case of \code{plot} further
}
\examples{
data(woodmouse)
-tr <- nj(dist.dna(woodmouse))
+f <- function(x) nj(dist.dna(x))
+tr <- f(woodmouse)
### Are bootstrap values stable?
for (i in 1:5)
- print(boot.phylo(tr, woodmouse, function(xx) nj(dist.dna(xx))))
+ print(boot.phylo(tr, woodmouse, f, quiet = TRUE))
### How many partitions in 100 random trees of 10 labels?...
TR <- replicate(100, rtree(10), FALSE)
pp10 <- prop.part(TR)
\alias{compar.gee}
\alias{print.compar.gee}
\alias{drop1.compar.gee}
+\alias{predict.compar.gee}
\title{Comparative Analysis with GEEs}
\description{
\code{compar.gee} performs the comparative analysis using generalized
\code{drop1} tests single effects of a fitted model output from
\code{compar.gee}.
+
+ \code{predict} returns the predicted (fitted) values of the model.
}
\usage{
compar.gee(formula, data = NULL, family = "gaussian", phy, corStruct,
scale.fix = FALSE, scale.value = 1)
\method{drop1}{compar.gee}(object, scope, quiet = FALSE, ...)
+\method{predict}{compar.gee}(object, type = c("link", "response"), ...)
}
\arguments{
\item{formula}{a formula giving the model to be fitted.}
\item{scope}{<unused>.}
\item{quiet}{a logical specifying whether to display a warning message
about eventual ``marginality principle violation''.}
+ \item{type}{a character string specifying the type of predicted
+ values. By default, the linear (link) prediction is returned.}
\item{\dots}{further arguments to be passed to \code{drop1}.}
}
\details{
--- /dev/null
+\name{evonet}
+\alias{evonet}
+\alias{print.evonet}
+\alias{plot.evonet}
+\alias{as.phylo.evonet}
+\alias{as.networx.evonet}
+\alias{as.network.evonet}
+\alias{as.igraph.evonet}
+\title{Evolutionary Networks}
+\description{
+ \code{evonet} builds a network from a tree of class
+ \code{"phylo"}. There are \code{print} and \code{plot} methods as well
+ as a few conversion functions.
+}
+\usage{
+evonet(phy, from, to = NULL)
+\method{print}{evonet}(x, ...)
+\method{plot}{evonet}(x, col = "blue", lty = 1, lwd = 1, alpha = 0.5,
+ arrows = 0, arrow.type = "classical", ...)
+\method{as.phylo}{evonet}(x, ...)
+\method{as.networx}{evonet}(x, weight = NA, ...)
+\method{as.network}{evonet}(x, directed = TRUE, ...)
+\method{as.igraph}{evonet}(x, directed = TRUE, use.labels = TRUE, ...)
+}
+\arguments{
+ \item{phy, x}{an object of class \code{"phylo"} or \code{"evonet"}.}
+ \item{from}{a vector (or a matrix if \code{to = NULL}) giving the node
+ or tip numbers involved in the reticulations.}
+ \item{to}{a vector of the same length than \code{from}.}
+ \item{col, lty, lwd}{colors, line type and width of the reticulations
+ (recycled if necessary).}
+ \item{alpha}{a value between 0 and 1 specifying the transparency of
+ the reticulations.}
+ \item{arrows}{see \code{\link{fancyarrows}}.}
+ \item{arrow.type}{idem.}
+ \item{weight}{a numeric vector giving the weights for the
+ reticulations when converting to the class \code{"networx"}
+ (recycled or shortened if needed).}
+ \item{directed}{a logical: should the network be considered as
+ directed? \code{TRUE} by default.}
+ \item{use.labels}{a logical specifying whether to use the tip and node
+ labels when building the network of class \code{"igraph"}.}
+ \item{\dots}{arguments passed to other methods.}
+}
+\details{
+ \code{evonet} is a constructor function that checks the arguments.
+
+ The classes \code{"networx"}, \code{"network"}, and \code{"igraph"}
+ are defined in the packages \pkg{phangorn}, \pkg{network}, and
+ \pkg{igraph}, respectively.
+}
+\value{
+ an object of class \code{c("evonet", "phylo")} which is made of an
+ object of class \code{"\link{phylo}"} plus an element
+ \code{reticulation} coding additional edges among nodes and uses the
+ same coding rules than the \code{edge} matrix.
+
+ The conversion functions return an object of the appropriate class.
+}
+\author{Emmanuel Paradis}
+\seealso{
+ \code{\link[phangorn]{as.networx}} in package \pkg{phangorn}
+}
+\examples{
+tr <- rcoal(5)
+(x <- evonet(tr, 6:7, 8:9))
+plot(x)
+}
+\keyword{manip}
+\keyword{hplot}
cex = par("cex"), adj = NULL, srt = 0, no.margin = FALSE,
root.edge = FALSE, label.offset = 0, underscore = FALSE,
x.lim = NULL, y.lim = NULL, direction = "rightwards",
- lab4ut = "horizontal", tip.color = "black", draw = TRUE, ...)
+ lab4ut = "horizontal", tip.color = "black", plot = TRUE, ...)
\method{plot}{multiPhylo}(x, layout = 1, ...)
}
\arguments{
\code{type = "unrooted"}.}
\item{tip.color}{the colours used for the tip labels, eventually
recycled (see examples).}
- \item{draw}{a logical controlling whether to draw the tree. If
+ \item{plot}{a logical controlling whether to draw the tree. If
\code{FALSE}, the graphical device is set as if the tree was
plotted, and the coordinates are saved as well.}
\item{layout}{the number of trees to be plotted simultaneously.}
tre.new <- rotate(tre, 30)
# compare the results:
-par(mfrow=c(1,2)) # devide graphical device
+par(mfrow=c(1,2)) # split graphical device
plot(tre) # plot old tre
plot(tre.new) # plot new tree
tre.new <- rotate(tre, c(12, 21))
# compare the results:
-par(mfrow=c(1,2)) # devide graphical device
+par(mfrow=c(1,2)) # split graphical device
plot(tre) # plot old tre
plot(tre.new) # plot new tree
\name{yule}
\alias{yule}
-\title{Fits Yule Model to a Phylogenetic Tree}
+\title{Fits the Yule Model to a Phylogenetic Tree}
\usage{
yule(phy, use.root.edge = FALSE)
}
projects / ape.git / commitdiff