1 CHANGES IN APE VERSION 3.0-2
6 o The new function alex (alignment explorator) zooms in a DNA
7 alignment and opens the result in a new window.
12 o compute.brtime() did not completely randomized the order of the
15 o write.nexus() did not work correctly with rooted trees (thanks
16 to Matt Johnson for the fix).
18 o mltt.plot(, backward = FALSE) did not set the x-axis correctly.
20 o A bug was introduced in prop.clades() with ape 3.0. The help page
21 has been clarified relative to the use of the option 'rooted'.
23 o mantel.test() printed a useless warning message.
25 o plot.phylo(, direction = "downward") ignored 'y.lim'.
27 o is.monophyletic() did not work correctly if 'tips' was not stored
30 o prop.part() could make R crash if the first tree had many
33 o njs(), bionjs(), and mvrs() now return an error if 'fs < 1'.
35 o SDM() did not work correctly. The code has also been generally
41 o The DESCRIPTION file has been updated.
43 o The option 'original.data' of write.nexus() has been removed.
45 o The files bionjs.c, mvr.c, mvrs.c, njs.c, triangMtd.c, and
46 triangMtds.c have been improved which should fix some bugs in
47 the corresponding functions.
51 CHANGES IN APE VERSION 3.0-1
56 o dist.dna() has two new models: "indel" and "indelblock".
58 o bind.tree() now accepts 'position' > 0 when the trees have no
59 banch length permitting to create a node in 'x' when grafting
60 'y' (see ?bind.tree for details).
65 o cophyloplot( , rotate = TRUE) made R hanged after a few clicks.
66 Also the tree is no more plotted twice.
68 o read.GenBank() has been updated to work with EFetch 2.0.
70 o unroot() on trees in "pruningwise" order did not respect this
75 CHANGES IN APE VERSION 3.0
80 o The three functions dyule, dbd, and dbdTime calculate the
81 density probability (i.e., the distribution of the number of
82 species) for the Yule, the constant and the time-dependent
83 birth-beath models, respectively. These probabilities can be
84 conditional on no extinction and/or on a log-scale.
86 o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
87 fan, or radial trees around the center of the plot.
89 o boot.phylo() and prop.clades() have a new option rooted =
90 FALSE. Note that the behaviour of prop.part() is unchanged.
92 o edgelabels() has a new option 'date' to place labels on edges of
93 chronograms using the time scale (suggestion by Rob Lanfear).
98 o In chronopl(), the code setting the initial dates failed in
99 complicated settings (several dates known within intervals).
100 This has been generally improved and should result in faster
101 and more efficient convergence even in simple settings.
103 o mantel.test() sometimes returned P-values > 1 with the default
106 o extract.clade() sometimes shuffled some tip labels (thanks to
107 Ludovic Mallet and Mahendra Mariadassou for the fix).
109 o clustal() should now find by default the executable under Windows.
114 o The code of yule() has been simplified and is now much faster for
117 o The code of mantel.test() has been adjusted to be consistent
118 with common permutation tests.
120 o The C code of base.freq() has been improved and is now nearly 8
123 o The option 'original.data' of write.nexus() is now deprecated and
124 will be removed in a future release.
126 o The code of is.ultrametric() has been improved and is now 3 times
129 o The code of vcv.phylo() has been improved and is now 10 or 30
130 times faster for 100 or 1000 tips, respectively. Consequently,
131 fitting models with PGLS will be faster overall.
135 CHANGES IN APE VERSION 2.8
140 o Twelve new functions have been written by Andrei-Alin Popescu:
141 additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
142 njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
144 o A new class "bitsplits" has been created by Andrei-Alin Popescu
145 to code splits (aka, bipartition).
147 o There is a new generic function as.bitsplits with a method to
148 convert from the class "prop.part" to the class "bitsplits".
150 o The new function ltt.coplot plots on the same scales a tree and
151 the derived LTT plot.
153 o ltt.plot() has two new options: backward and tol. It can now
154 handle non-ultrametic trees and its internal coding has been
155 improved. The coordinates of the plot can now be computed with
156 the new function ltt.plot.coords.
161 o prop.part() crashed if some trees had some multichotomies.
165 CHANGES IN APE VERSION 2.7-3
170 o The new function compute.brtime computes and sets branching times.
172 o mantel.test() has a new argument 'alternative' which is
173 "two-sided" by default. Previously, this test was one-tailed
174 with no possibility to change.
176 o ace() can now do REML estimation with continuous characters,
177 giving better estimates of the variance of the Brownian motion
183 o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
184 position = 0). (Thanks to Liam Revell for digging this bug out.)
186 o Simulation of OU process with rTraitCont() did not work correctly.
187 This now uses formula from Gillespie (1996) reduced to a BM
188 process when alpha = 0 to avoid division by zero. The option
189 'linear' has been removed.
191 o Cross-validation in chronopl() did not work when 'age.max' was
194 o consensus(, p = 0.5) could return an incorrect tree if some
195 incompatible splits occur in 50% of the trees (especially with
196 small number of trees).
198 o c() with "multiPhylo" did not work correctly (thanks to Klaus
199 Schliep for the fix).
201 o root() failed in some cases with an outgroup made of several tips.
202 The help page has been clarified a bit.
206 CHANGES IN APE VERSION 2.7-2
211 o There is a new class "evonet" to code evolutionary networks, with
212 a constructor function evonet(), a print() and a plot() methods,
213 and four conversion methods to the classes "phylo", "networx",
214 "network", and "igraph".
216 o The new function rTraitMult does multivariate traits simulation
217 with user-defined models.
219 o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
220 is not plotted but the graphical device is set and the
221 coordinates are saved as usual.
223 o diversity.contrast.test() gains a fourth version of the test with
224 method = "logratio"; the literature citations have been clarified.
226 o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
227 the aspect of the bar.
229 o boot.phylo() now displays a progress bar by default (can be off
232 o There is a new predict() method for compar.gee().
237 o bionj() made R crash if distances were too large. It now returns
238 an error if at least one distance is greater than 100.
240 o drop.tip() returned a wrong tree if 'tip' was of zero length.
242 o read.nexus.data() failed with URLs.
244 o boot.phylo() returned overestimated support values in the
245 presence of identical or nearly identical sequences.
250 o The data bird.families, bird.orders, cynipids, and woodmouse are
251 now provided as .rda files.
255 CHANGES IN APE VERSION 2.7-1
260 o The new function trex does tree exploration with multiple
263 o The new function kronoviz plots several rooted (dated) trees on
266 o identify.phylo() has a new option 'quiet' (FALSE by default).
271 o A bug was introduced in read.nexus() in ape 2.7.
273 o image.DNAbin() did not colour correctly the bases if there were
276 o .compressTipLabel() failed with a list with a single tree.
278 o identify.phylo() returned a wrong answer when the x- and y-scales
281 o write.nexus() failed with lists of trees with compressed labels.
286 o identify.phylo() now returns NULL if the user right- (instead of
287 left-) clicks (an error was returned previously).
289 o read.nexus() should be robust to commands inserted in the TREES
294 CHANGES IN APE VERSION 2.7
299 o There is a new image() method for "DNAbin" objects: it plots DNA
300 alignments in a flexible and efficient way.
302 o Two new functions as.network.phylo and as.igraph.phylo convert
303 trees of class "phylo" into these respective network classes
304 defined in the packages of the same names.
306 o The three new functions clustal, muscle, and tcoffee perform
307 nucleotide sequence alignment by calling the external programs
310 o Four new functions, diversity.contrast.test, mcconwaysims.test,
311 richness.yule.test, and slowinskiguyer.test, implement various
312 tests of diversification shifts using sister-clade comparisons.
314 o base.freq() gains an option 'all' to count all the possible bases
315 including the ambiguous ones (defaults to FALSE).
317 o read.nexus() now writes tree names in the NEXUS file if given a
318 list of trees with names.
323 o prop.part() failed in some situations with unrooted trees.
325 o read.nexus() shuffled node labels when a TRANSLATE block was
328 o varCompPhylip() did not work if 'exec' was specified.
330 o bind.tree() shuffled node labels when position > 0 and 'where'
336 o BaseProportion in src/dist_dna.c has been modified.
338 o A number of functions in src/tree_build.c have been modified.
340 o The matching representation has now only two columns as the third
341 column was redundant.
345 CHANGES IN APE VERSION 2.6-3
350 o rTraitCont() and rTraitDisc() gains a '...' argument used with
351 user-defined models (suggestion by Gene Hunt).
356 o as.hclust.phylo() now returns an error with unrooted trees.
358 o as.hclust.phylo() failed with trees with node labels (thanks to
359 Jinlong Zhang for pointing this bug out).
361 o read.dna(, "fasta") failed if sequences were not all of the same
364 o plot.phylo() did not recycle values of 'font', 'cex' and
365 'tip.color' correctly when type = "fan" or "radial".
367 o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
368 "unrooted" with lab4ut = "axial" (the placement of tip labels still
369 needs to be improved with lab4ut = "horizontal").
374 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
376 o The help command ?phylo now points to the man page of read.tree()
377 where this class is described. Similarly, ?matching points to the
378 man page of as.matching().
382 CHANGES IN APE VERSION 2.6-2
387 o Two new functions, pic.ortho and varCompPhylip, implements the
388 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
389 second function requires Phylip to be installed on the computer.
391 o bd.ext() has a new option conditional = TRUE to use probabilities
392 conditioned on no extinction for the taxonomic data.
397 o write.tree() failed to output correctly tree names.
399 o dist.nodes() returned duplicated column(s) with unrooted and/or
400 multichotomous trees.
402 o mcmc.popsize() terminated unexpectedly if the progress bar was
405 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
407 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
409 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
412 o Objects returned by as.hclust.phylo() failed when analysed with
413 cutree() or rect.hclust().
415 o write.tree() did not output correctly node labels (thanks to Naim
416 Matasci and Jeremy Beaulieu for the fix).
418 o ace(type = "discrete") has been improved thanks to Naim Marasci and
423 CHANGES IN APE VERSION 2.6-1
428 o The new function speciesTree calculates the species tree from a set
429 of gene trees. Several methods are available including maximum tree
430 and shallowest divergence tree.
435 o A bug introduced in write.tree() with ape 2.6 has been fixed.
437 o as.list.DNAbin() did not work correctly with vectors.
439 o as.hclust.phylo() failed with trees with node labels (thanks to
440 Filipe Vieira for the fix).
444 CHANGES IN APE VERSION 2.6
449 o The new functions rlineage and rbdtree simulate phylogenies under
450 any user-defined time-dependent speciation-extinction model. They
451 use continuous time algorithms.
453 o The new function drop.fossil removes the extinct species from a
456 o The new function bd.time fits a user-defined time-dependent
457 birth-death model. It is a generalization of yule.time() taking
458 extinction into account.
460 o The new function MPR does most parsimonious reconstruction of
463 o The new function Ftab computes the contingency table of base
464 frequencies from a pair of sequences.
466 o There is now an 'as.list' method for the class "DNAbin".
468 o dist.dna() can compute the number of transitions or transversions
469 with the option model = "Ts" or model = "Tv", respectively.
471 o [node|tip|edge]labels() gain three options with default values to
472 control the aspect of thermometers: horiz = TRUE, width = NULL,
475 o compar.gee() has been improved with the new option 'corStruct' as an
476 alternative to 'phy' to specify the correlation structure, and
477 calculation of the QIC (Pan 2001, Biometrics). The display of the
478 results has also been improved.
480 o read.GenBank() has a new option 'gene.names' to return the name of
481 the gene (FALSE by default).
486 o extract.clade() sometimes shuffled the tip labels.
488 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
491 o dist.dna(model = "logdet") used to divide distances by 4. The
492 documentation has been clarified on the formulae used.
497 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
498 change the parameterisation (see ?rTraitCont for details).
500 o pic() now returns a vector with the node labels of the tree (if
503 o write.tree() and read.tree() have been substantially improved thanks
504 to contributions by Klaus Schliep.
508 CHANGES IN APE VERSION 2.5-3
513 o The new function mixedFontLabel helps to make labels with bits of
514 text to be plotted in different fonts.
516 o There are now replacement operators for [, [[, and $ for the class
517 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
518 check that the tip labels are the same in all trees.
520 o Objects of class "multiPhylo" can be built with c(): there are
521 methods for the classes "phylo" and "multiPhylo".
523 o The internal functions .compressTipLabel and .uncompressTipLabel are
529 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
530 was a single-edge tree and 'where' was a tip.
532 o rTraitCont() did not use the square-root of branch lengths when
533 simulating a Brownian motion model.
537 CHANGES IN APE VERSION 2.5-2
542 o There is now a print method for results from ace().
544 o There is a labels() method for objects of class "DNAbin".
546 o read.dna() has a new option 'as.matrix' to possibly force sequences
547 in a FASTA file to be stored in a matrix (see ?read.dna for details).
552 o as.phylo.hclust() used to multiply edge lengths by 2.
554 o A minor bug was fixed in rTraitDisc().
556 o ace() sometimes failed (parameter value was NaN and the optimisation
562 o evolve.phylo() and plot.ancestral() have been removed.
564 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
569 o nj() has been improved and is now about 30% faster.
571 o The default option 'drop' of [.DNAbin has been changed to FALSE to
572 avoid dropping rownames when selecting a single sequence.
574 o print.DNAbin() has been changed to summary.DNAbin() which has been
579 CHANGES IN APE VERSION 2.5-1
584 o The new function stree generates trees with regular shapes.
586 o It is now possible to bind two trees with x + y (see ?bind.tree for
589 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
590 'interactive' option to make the operation on a plotted tree.
592 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
593 association links; they are recycled like 'col' (which wasn't before).
598 o rTraitDisc() did not use its 'freq' argument correctly (it was
599 multiplied with the rate matrix column-wise instead of row-wise).
601 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
602 with NA values. Nothing is drawn now like with 'text' or 'pch'.
603 The same bug occurred with the 'pie' option.
605 o A bug was fixed in compar.ou() and the help page was clarified.
607 o bind.tree() has been rewritten fixing several bugs and making it
610 o plot.phylo(type = "p") sometimes failed to colour correctly the
611 vertical lines representing the nodes.
613 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
614 in the correct direction though the tip labels were displayed
620 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
621 the sequences are correctly stored (in a list for c, in a matrix
622 for the two other functions).
626 CHANGES IN APE VERSION 2.5
631 o The new function parafit by Pierre Legendre tests for the
632 coevolution between hosts and parasites. It has a companion
633 function, pcoa, that does principal coordinate decomposition.
634 The latter has a biplot method.
636 o The new function lmorigin by Pierre Legendre performs multiple
637 regression through the origin with testing by permutation.
639 o The new functions rTraitCont and rTraitDisc simulate continuous and
640 discrete traits under a wide range of evolutionary models.
642 o The new function delta.plot does a delta plot following Holland et
643 al. (2002, Mol. Biol. Evol. 12:2051).
645 o The new function edges draws additional branches between any nodes
646 and/or tips on a plotted tree.
648 o The new function fancyarrows enhances arrows from graphics with
649 triangle and harpoon heads; it can be called from edges().
651 o add.scale.bar() has a new option 'ask' to draw interactively.
653 o The branch length score replaces the geodesic distance in dist.topo.
655 o Three new data sets are included: the gopher-lice data (gopher.D),
656 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
657 Rohlf 1995), and some host-parasite specificity data
658 (lmorigin.ex2, from Legendre & Desdevises 2009).
663 o add.scale.bar() drew the bar outside the plotting region with the
664 default options with unrooted or radial trees.
666 o dist.topo() made R stuck when the trees had different sizes (thanks
667 to Otto Cordero for the fix).
672 o The geodesic distance has been replaced by the branch length score
677 CHANGES IN APE VERSION 2.4-1
682 o rtree() and rcoal() now accept a numeric vector for the 'br'
685 o vcv() is a new generic function with methods for the classes "phylo"
686 and "corPhyl" so that it is possible to calculate the var-cov matrix
687 for "transformation models". vcv.phylo() can still be used for trees
688 of class "phylo"; its argument 'cor' has been renamed 'corr'.
693 o bind.tree() failed when 'y' had no root edge.
695 o read.nexus() shuffled tip labels when the trees have no branch
696 lengths and there is a TRANSLATE block.
698 o read.nexus() does not try to translate node labels if there is a
699 translation table in the NEXUS file. See ?read.nexus for a
700 clarification on this behaviour.
702 o plot.multiPhylo() crashed R when plotting a list of trees with
703 compressed tip labels.
705 o write.nexus() did not translate the taxa names when asked for.
707 o plot.phylo(type = "fan") did not rotate the tip labels correctly
708 when the tree has branch lengths.
710 o ace(type = "continuous", method = "ML") now avoids sigma² being
711 negative (which resulted in an error).
713 o nj() crashed with NA/NaN in the distance matrix: an error in now
718 CHANGES IN APE VERSION 2.4
723 o base.freq() has a new option 'freq' to return the counts; the
724 default is still to return the proportions.
729 o seg.sites() did not handle ambiguous nucleotides correctly: they
732 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
733 the tree: the argument is now ignored.
735 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
741 o Trying to plot a tree with a single tip now returns NULL with a
742 warning (it returned an error previously).
744 o The way lines representing nodes are coloured in phylograms has
745 been modified (as well as their widths and types) following some
746 users' request; this is only for dichotomous nodes.
748 o The argument 'adj' in [node][tip][edge]labels() now works when
749 using 'pie' or 'thermo'.
751 o A more informative message error is now returned by dist.dna() when
752 'model' is badly specified (partial matching of this argument is
755 o Deprecated functions are now listed in a help page: see
756 help("ape-defunct") with the quotes.
761 o The functions heterozygosity, nuc.div, theta.h, theta.k and
762 theta.s have been moved from ape to pegas.
764 o The functions mlphylo, DNAmodel and sh.test have been removed.
768 CHANGES IN APE VERSION 2.3-3
773 o add.scale.bar() always drew a horizontal bar.
775 o zoom() shuffled tips with unrooted trees.
777 o write.nexus() failed to write correctly trees with a "TipLabel"
780 o rcoal() failed to compute branch lengths with very large n.
782 o A small bug was fixed in compar.cheverud() (thanks to Michael
785 o seg.sites() failed when passing a vector.
787 o drop.tip() sometimes shuffled tip labels.
789 o root() shuffled node labels with 'resolve.root = TRUE'.
793 CHANGES IN APE VERSION 2.3-2
798 o all.equal.phylo() did not compare unrooted trees correctly.
800 o dist.topo(... method = "PH85") did not treat unrooted trees
801 correctly (thanks to Tim Wallstrom for the fix).
803 o root() sometimes failed to test for the monophyly of the
806 o extract.clade() sometimes included too many edges.
808 o vcv.phylo() did not work correctly when the tree is in
811 o nj() did not handle correctly distance matrices with many 0's.
812 The code has also been significantly improved: 7, 70, 160 times
813 faster with n = 100, 500, 1000, respectively.
817 CHANGES IN APE VERSION 2.3-1
822 o The new function is.monophyletic tests the monophyly of a group.
824 o There is now a c() method for lists of class "DNAbin".
826 o yule.cov() now fits the null model, and its help page has been
827 corrected with respect to this change.
829 o drop.tip() has a new option 'rooted' to force (or not) a tree
830 to be treated as (un)rooted.
835 o dist.gene() failed on most occasions with the default
836 pairwise.deletion = FALSE.
838 o read.tree() failed to read correctly the tree name(s).
840 o boot.phylo() now treats correctly data frames.
842 o del.gaps() did not copy the rownames of a matrix.
844 o A small bug was fixed in CDAM.global().
846 o ace() failed with large data sets. Thanks to Rich FitzJohn for
847 the fix. With other improvements, this function is now about 6
850 o write.tree() failed with objects of class "multiPhylo".
852 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
857 o [.multiPhylo and [.DNAbin now respect the original class.
859 o Instances of the form class(phy) == "phylo" have been replaced
860 by inherits(phy, "phylo").
862 o rcoal() is now faster.
867 o klastorin() has been removed.
871 CHANGES IN APE VERSION 2.3
876 o The new functions CADM.global and CADM.post, contributed by
877 Pierre Legendre, test the congruence among several distance
880 o The new function yule.time fits a user-defined time-dependent
881 Yule model by maximum likelihood.
883 o The new function makeNodeLabel creates and/or modifies node
884 labels in a flexible way.
886 o read.tree() and write.tree() have been modified so that they can
887 handle individual tree names.
889 o plot.phylo() has a new argument 'edge.lty' that specifies the
890 types of lines used for the edges (plain, dotted, dashed, ...)
892 o phymltest() has been updated to work with PhyML 3.0.1.
897 o drop.tip() shuffled tip labels in some cases.
899 o drop.tip() did not handle node.label correctly.
901 o is.ultrametric() now checks the ordering of the edge matrix.
903 o ace() sometimes returned negative values of likelihoods of
904 ancestral states (thanks to Dan Rabosky for solving this long
910 o The data set xenarthra has been removed.
914 CHANGES IN APE VERSION 2.2-4
918 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
919 now fixed. (Thanks to Peter Wragg for the fix!)
921 o A warning message occurred for no reason with ace(method="GLS").
926 o There is now a general help page displayed with '?ape'.
930 CHANGES IN APE VERSION 2.2-3
935 o The new function extract.clade extracts a clade from a tree by
936 specifying a node number or label.
938 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
939 operations of the same names.
941 o dist.dna() can now return the number of site differences by
942 specifying model="N".
947 o chronopl() did not work with CV = TRUE.
949 o read.nexus() did not work correctly in some situations (trees on
950 multiple lines with different numbers of lines and/or with
951 comments inserted within the trees).
953 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
954 the number of lineages with non-binary trees.
959 o ape has now a namespace.
961 o drop.tip() has been improved: it should be much faster and work
962 better in some cases (e.g., see the example in ?zoom).
966 CHANGES IN APE VERSION 2.2-2
971 o dist.gene() has been substantially improved and gains an option
974 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
980 o prop.part() failed with a single tree with the default option
981 'check.labels = TRUE'.
983 o summary.DNAbin() failed to display correctly the summary of
984 sequence lengths with lists of sequences of 10,000 bases or more
985 (because summary.default uses 4 significant digits by default).
987 o read.nexus() failed to read a file with a single tree with line
988 breaks in the Newick string.
990 o del.gaps() returned a list of empty sequences when there were no
996 o phymltest() has been updated for PhyML 3.0 and gains an option
997 'append', whereas the option 'path2exec' has been removed.
999 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
1000 which is returned unchanged (instead of an error).
1002 o The data sets bird.orders and bird.families are now stored as
1003 Newick strings; i.e., the command data(bird.orders) calls
1008 CHANGES IN APE VERSION 2.2-1
1013 o The new function makeLabel() helps to modify labels of trees,
1014 lists of trees, or DNA sequences, with several utilities to
1015 truncate and/or make them unique, substituting some
1016 characters, and so on.
1018 o The new function del.gaps() removes insertion gaps ("-") in a
1019 set of DNA sequences.
1021 o read.dna() can now read Clustal files (*.aln).
1026 o root() failed with 'resolve.root = TRUE' when the root was
1027 already the specified root.
1029 o Several bugs were fixed in mlphylo().
1031 o collapsed.singles() did not propagate the 'Nnode' and
1032 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
1034 o read.nexus() failed to remove correctly the comments within
1037 o read.nexus() failed to read a file with a single tree and no
1038 translation of tip labels.
1040 o read.nexus() failed to place correctly tip labels when reading
1041 a single tree with no edge lengths.
1043 o A bug was fixed in sh.test().
1048 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
1051 o The option 'check.labels' of consensus() and prop.part() is now
1054 o write.dna() now does not truncate names to 10 characters with
1059 CHANGES IN APE VERSION 2.2
1064 o Four new functions have been written by Damien de Vienne for the
1065 graphical exploration of large trees (cophyloplot, subtrees,
1066 subtreeplot), and to return the graphical coordinates of tree
1069 o The new functions corPagel and corBlomberg implement the Pagel's
1070 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
1072 o chronopl() has been improved and gains several options: see its
1073 help page for details.
1075 o boot.phylo() has now an option 'trees' to possibly return the
1076 bootstraped trees (the default is FALSE).
1078 o prop.part() has been improved and should now be faster in all
1084 o read.dna() failed if "?" occurred in the first 10 sites of the
1087 o The x/y aspect of the plot is now respected when plotting a
1088 circular tree (type = "r" or "f").
1090 o Drawing the tip labels sometimes failed when plotting circular
1093 o zoom() failed when tip labels were used instead of their numbers
1094 (thanks to Yan Wong for the fix).
1096 o drop.tip() failed with some trees (fixed by Yan Wong).
1098 o seg.sites() failed with a list.
1100 o consensus() failed in some cases. The function has been improved
1101 as well and is faster.
1105 CHANGES IN APE VERSION 2.1-3
1110 o A bug in read.nexus() made the Windows R-GUI crash.
1112 o An error was fixed in the computation of ancestral character
1113 states by generalized least squares in ace().
1115 o di2multi() did not modify node labels correctly.
1117 o multi2di() failed if the tree had its attribute "order" set to
1122 CHANGES IN APE VERSION 2.1-2
1127 o There three new methods for the "multiPhylo" class: str, $,
1130 o root() gains the options 'node' and 'resolve.root'
1131 (FALSE by default) as well as its code being improved.
1133 o mltt.plot() has now an option 'log' used in the same way
1134 than in plot.default().
1139 o mltt.plot() failed to display the legend with an unnamed
1142 o nodelabels() with pies now correcly uses the argument
1143 'cex' to draw symbols of different sizes (which has
1144 worked already for thermometers).
1146 o read.nexus() generally failed to read very big files.
1151 o The argument 'family' of compar.gee() can now be a function
1152 as well as a character string.
1154 o read.tree() and read.nexus() now return an unnamed list if
1155 'tree.names = NULL'.
1157 o read.nexus() now returns a modified object of class "multiPhylo"
1158 when there is a TRANSLATE block in the NEXUS file: the individual
1159 trees have no 'tip.label' vector, but the list has a 'TipLabel'
1160 attribute. The new methods '$' and '[[' set these elements
1161 correctly when extracting trees.
1165 CHANGES IN APE VERSION 2.1-1
1170 o The new function rmtree generates lists of random trees.
1172 o rcoal() now generates a genuine coalescent tree by default
1173 (thanks to Vladimir Minin for the code).
1178 o nuc.div() returned an incorrect value with the default
1179 pairwise.deletion = FALSE.
1184 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
1185 have been improved so that they are stabler and faster.
1187 o R packages used by ape are now loaded silently; lattice and gee
1188 are loaded only when needed.
1192 CHANGES IN APE VERSION 2.1
1197 o The new function identify.phylo identifies clades on a plotted
1198 tree using the mouse.
1200 o It is now possible to subset a list of trees (object of class
1201 "multiPhylo") with "[" while keeping its class correct.
1203 o The new function as.DNAbin.alignment converts DNA sequences
1204 stored in the "alignment" format of the package seqinr into
1205 an object of class "DNAbin".
1207 o The new function weight.taxo2 helps to build similarity matrices
1208 given two taxonomic levels (usually called by other functions).
1210 o write.tree() can now take a list of trees (class "multiPhylo")
1211 as its main argument.
1213 o plot.correlogram() and plot.correlogramList() have been
1214 improved, and gain several options (see the help page for
1215 details). A legend is now plotted by default.
1220 o dist.dna() returned some incorrect values with `model = "JC69"'
1221 and `pairwise.deletion = TRUE'. This affected only the
1222 distances involving sequences with missing values. (Thanks
1223 to Bruno Toupance for digging this bug out.)
1225 o write.tree() failed with some trees: this is fixed by removing
1226 the `multi.line' option (trees are now always printed on a
1229 o read.nexus() did not correctly detect trees with multiple root
1230 edges (see OTHER CHANGES).
1235 o The code of mlphylo() has been almost entirely rewritten, and
1236 should be much stabler. The options have been also greatly
1237 simplified (see ?mlphylo and ?DNAmodel for details).
1239 o The internal function nTips has been renamed klastorin_nTips.
1241 o The code of is.ultrametric() contained redundancies and has
1244 o The code of Moran.I() and of correlogram.formula() have been
1247 o read.tree() and read.nexus() now return an error when trying to
1248 read a tree with multiple root edges (see BUG FIXES). The
1249 correction applied in previous version did not work in all
1252 o The class c("multi.tree", "phylo") has been renamed
1258 o There is now a vignette in ape: see vignette("MoranI", "ape").
1261 DEPRECATED & DEFUNCT
1263 o as.matching() and as.phylo.matching() do not support branch
1266 o correlogram.phylo() and discrete.dist() have been removed.
1270 CHANGES IN APE VERSION 2.0-2
1275 o The new function matexpo computes the exponential of a square
1278 o The new function unique.multi.tree removes duplicate trees from
1281 o yule() has a new option `use.root.edge = FALSE' that specifies
1282 to ignore, by default, the root edge of the tree if it exists.
1287 o which.edge() failed when the index of a single terminal edge was
1290 o In diversi.time(), the values returned for model C were
1293 o A bug was fixed in yule() that affected the calculation of the
1294 likelihood in the presence of ties in the branching times.
1296 o There was a bug in the C function mat_expo4x4 affecting the
1297 calculations of the transition probabilities for models HKY and
1300 o A small bug was fixed in as.matrix.DNAbin (thanks to James
1303 o rtree() did not `shuffle' the tip labels by default, so only a
1304 limited number of labelled topologies could be generated.
1308 CHANGES IN APE VERSION 2.0-1
1313 o The three new functions bionj, fastme.ols, and fastme.bal
1314 perform phylogeny estimation by the BIONJ and fastME methods in
1315 OLS and balanced versions. This is a port to R of previous
1316 previous programs done by Vincent Lefort.
1318 o The new function chronoMPL performs molecular dating with the
1319 mean path lengths method of Britton et al. (2002, Mol. Phyl.
1322 o The new function rotate, contributed by Christoph Heibl, swaps
1323 two clades connected to the same node. It works also with
1324 multichotomous nodes.
1326 o The new `method' as.matrix.DNAbin() may be used to convert
1327 easily DNA sequences stored in a list into a matrix while
1328 keeping the names and the class.
1333 o chronopl() failed when some branch lengths were equal to zero:
1334 an error message is now returned.
1336 o di2multi() failed when there was a series of consecutive edges
1341 CHANGES IN APE VERSION 1.10-2
1346 o plot.phylo() can now plot circular trees: the option is type =
1347 "fan" or type = "f" (to avoid the ambiguity with type = "c").
1349 o prop.part() has a new option `check.labels = FALSE' which allows
1350 to considerably speed-up the calculations of bipartitions. As a
1351 consequence, calculations of bootstrap values with boot.phylo()
1352 should be much faster.
1357 o read.GenBank() did not return correctly the list of species as
1358 from ape 1.10: this is fixed in this version
1360 o Applying as.phylo() on a tree of class "phylo" failed: the
1361 object is now returned unchanged.
1365 CHANGES IN APE VERSION 1.10-1
1370 o The three new functions Ntip, Nnode, and Nedge return, for a
1371 given tree, the number of tips, nodes, or edges, respectively.
1376 o read.nexus() did not set correctly the class of the returned
1377 object when reading multiple trees.
1379 o mllt.plot() failed with objects of class c("multi.tree",
1382 o unroot() did not work correctly in most cases.
1384 o reorder.phylo() made R freeze in some occasions.
1386 o Plotting a tree in pruningwise order failed.
1388 o When plotting an unrooted tree, the tip labels where not all
1389 correctly positioned if the option `cex' was used.
1393 CHANGES IN APE VERSION 1.10
1398 o Five new `method' functions have been introduced to manipulate
1399 DNA sequences in binary format (see below).
1401 o Three new functions have been introduced to convert between the
1402 new binary and the character formats.
1404 o The new function as.alignment converts DNA sequences stored as
1405 single characters into the class "alignment" used by the package
1408 o read.dna() and read.GenBank() have a new argument `as.character'
1409 controlling whether the sequences are returned in binary format
1415 o root() failed when the tree had node labels: this is fixed.
1417 o plot.phylo() did not correctly set the limits on the y-axis with
1418 the default setting: this is fixed.
1420 o dist.dna() returned a wrong result for the LogDet, paralinear,
1421 and BH87 models with `pairwise.deletion = TRUE'.
1426 o DNA sequences are now internally stored in a binary format. See
1427 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1428 details. Most functions analyzing DNA functions have been
1429 modified accordingly and are now much faster (dist.dna is now
1430 ca. 60 times faster).
1434 CHANGES IN APE VERSION 1.9-4
1439 o A bug was fixed in edgelabels().
1441 o as.phylo.hclust() did not work correctly when the object of
1442 class "hclust" has its labels set to NULL: the returned tree has
1443 now its tip labels set to "1", "2", ...
1445 o consensus could fail if some tip labels are a subset of others
1446 (e.g., "a" and "a_1"): this is now fixed.
1448 o mlphylo() failed in most cases if some branch lengths of the
1449 initial tree were greater than one: an error message is now
1452 o mlphylo() failed in most cases when estimating the proportion of
1453 invariants: this is fixed.
1457 CHANGES IN APE VERSION 1.9-3
1462 o The new function edgelabels adds labels on the edge of the tree
1463 in the same way than nodelabels or tiplabels.
1468 o multi2di() did not handle correctly branch lengths with the
1469 default option `random = TRUE': this is now fixed.
1471 o A bug was fixed in nuc.div() when using pairwise deletions.
1473 o A bug occurred in the analysis of bipartitions with large
1474 numbers of large trees, with consequences on prop.part,
1475 prop.clades, and boot.phylo.
1477 o The calculation of the Billera-Holmes-Vogtmann distance in
1478 dist.topo was wrong: this has been fixed.
1482 CHANGES IN APE VERSION 1.9-2
1487 o The new function ladderize reorganizes the internal structure of
1488 a tree to plot them left- or right-ladderized.
1490 o The new function dist.nodes computes the patristic distances
1491 between all nodes, internal and terminal, of a tree. It replaces
1492 the option `full = TRUE' of cophenetic.phylo (see below).
1497 o A bug was fixed in old2new.phylo().
1499 o Some bugs were fixed in chronopl().
1501 o The edge colours were not correctly displayed by plot.phylo
1502 (thank you to Li-San Wang for the fix).
1504 o cophenetic.phylo() failed with multichotomous trees: this is
1510 o read.dna() now returns the sequences in a matrix if they are
1511 aligned (interleaved or sequential format). Sequences in FASTA
1512 format are still returned in a list.
1514 o The option `full' of cophenetic.phylo() has been removed because
1515 it could not be used from the generic.
1518 DEPRECATED & DEFUNCT
1520 o rotate() has been removed; this function did not work correctly
1525 CHANGES IN APE VERSION 1.9-1
1530 o Trees with a single tip were not read correctly in R as the
1531 element `Nnode' was not set: this is fixed.
1533 o unroot() did not set correctly the number of nodes of the
1534 unrooted tree in most cases.
1536 o read.GenBank() failed when fetching very long sequences,
1537 particularly of the BX-series.
1539 o A bug was introduced in read.tree() with ape 1.9: it has been
1544 CHANGES IN APE VERSION 1.9
1549 o There are two new print `methods' for trees of class "phylo" and
1550 lists of trees of class "multi.tree", so that they are now
1551 displayed in a compact and informative way.
1553 o There are two new functions, old2new.phylo and new2old.phylo,
1554 for converting between the old and new coding of the class
1557 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1558 LogDet ("logdet"), and paralinear ("paralin").
1560 o compute.brlen() has been extended: several methods are now
1561 available to compute branch lengths.
1563 o write.dna() can now handle matrices as well as lists.
1568 o cophenetic.phylo() sometimes returned a wrong result with
1569 multichotomous trees: this is fixed.
1571 o rotate() failed when a single tip was specified: the tree is now
1574 o ace() did not return the correct index matrix with custom
1575 models: this is fixed.
1577 o multi2di() did not work correctly when resolving multichotomies
1578 randomly: the topology was always the same, only the arrangement
1579 of clades was randomized: this is fixed. This function now
1580 accepts trees with no branch lengths.
1582 o The output of diversi.gof() was blurred by useless prints when a
1583 user distribution was specified. This has been corrected, and
1584 the help page of this function has been expanded.
1589 o The internal structure of the class "phylo" has been changed:
1590 see the document "Definition of Formats for Coding Phylogenetic
1591 Trees in R" for the details. In addition, the code of most
1592 functions has been improved.
1594 o Several functions have been improved by replacing some R codes
1595 by C codes: pic, plot.phylo, and reorder.phylo.
1597 o There is now a citation information: see citation("ape") in R.
1599 o write.tree() now does not add extra 0's to branch lengths so
1600 that 1.23 is printed "1.23" by default, not "1.2300000000".
1602 o The syntax of bind.tree() has been simplified. This function now
1603 accepts trees with no branch lengths, and handles correctly node
1606 o The option `as.numeric' of mrca() has been removed.
1608 o The unused options `format' and `rooted' of read.tree() have
1611 o The unused option `format' of write.tree() has been removed.
1613 o The use of node.depth() has been simplified.
1617 CHANGES IN APE VERSION 1.8-5
1622 o Two new functions read.nexus.data() and write.nexus.data(),
1623 contributed by Johan Nylander, allow to read and write molecular
1624 sequences in NEXUS files.
1626 o The new function reorder.phylo() reorders the internal structure
1627 of a tree of class "phylo". It is used as the generic, e.g.,
1630 o read.tree() and read.nexus() can now read trees with a single
1633 o The new data set `cynipids' supplies a set of protein sequences
1639 o The code of all.equal.phylo() has been completely rewritten
1640 (thanks to Benoît Durand) which fixes several bugs.
1642 o read.tree() and read.nexus() now checks the labels of the tree
1643 to remove or substitute any characters that are illegal in the
1644 Newick format (parentheses, etc.)
1646 o A negative P-value could be returned by mantel.test(): this is
1651 CHANGES IN APE VERSION 1.8-4
1656 o The new function sh.test() computes the Shimodaira-
1659 o The new function collapse.singles() removes the nodes with a
1660 single descendant from a tree.
1662 o plot.phylo() has a new argument `tip.color' to specify the
1663 colours of the tips.
1665 o mlphylo() has now an option `quiet' to control the display of
1666 the progress of the analysis (the default is FALSE).
1671 o read.dna() did not read correctly sequences in sequential format
1672 with leading alignment gaps "-": this is fixed.
1674 o ace() returned a list with no class so that the generic
1675 functions (anova, logLik, ...) could not be used directly. This
1676 is fixed as ace() now returns an object of class "ace".
1678 o anova.ace() had a small bug when computing the number of degrees
1679 of freedom: this is fixed.
1681 o mlphylo() did not work when the sequences were in a matrix or
1682 a data frame: this is fixed.
1684 o rtree() did not work correctly when trying to simulate an
1685 unrooted tree with two tips: an error message is now issued.
1690 o The algorithm of rtree() has been changed: it is now about 40,
1691 100, and 130 times faster for 10, 100, and 1000 tips,
1696 CHANGES IN APE VERSION 1.8-3
1701 o There are four new `method' functions to be used with the
1702 results of ace(): logLik(), deviance(), AIC(), and anova().
1704 o The plot method of phymltest has two new arguments: `main' to
1705 change the title, and `col' to control the colour of the
1706 segments showing the AIC values.
1708 o ace() has a new argument `ip' that gives the initial values used
1709 in the ML estimation with discrete characters (see the examples
1710 in ?ace). This function now returns a matrix giving the indices
1711 of the estimated rates when analysing discrete characters.
1713 o nodelabels() and tiplabels() have a new argument `pie' to
1714 represent proportions, with any number of categories, as
1715 piecharts. The use of the option `thermo' has been improved:
1716 there is now no limitation on the number of categories.
1721 o mlphylo() did not work with more than two partitions: this is
1724 o root() failed if the proposed outgroup was already an outgroup
1725 in the tree: this is fixed.
1727 o The `col' argument in nodelabels() and tiplabels() was not
1728 correctly passed when `text' was used: this is fixed.
1730 o Two bugs were fixed in mlphylo(): parameters were not always
1731 correctly output, and the estimation failed in some cases.
1733 o plot.phylo() was stuck when given a tree with a single tip: this
1734 is fixed and a message error is now returned.
1736 o An error was corrected in the help page of gammaStat regarding
1737 the calculation of P-values.
1739 o Using gls() could crash R when the number of species in the tree
1740 and in the variables were different: this is fixed.
1744 CHANGES IN APE VERSION 1.8-2
1749 o The new function mlphylo() fits a phylogenetic tree by maximum
1750 likelihood from DNA sequences. Its companion function DNAmodel()
1751 is used to define the substitution model which may include
1752 partitioning. There are methods for logLik(), deviance(), and
1753 AIC(), and the summary() method has been extended to display in
1754 a friendly way the results of this model fitting. Currently, the
1755 functionality is limited to estimating the substitution and
1756 associated parameters and computing the likelihood.
1758 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1759 tests for single effects in GEE-based comparative method. A
1760 warning message is printed if there is not enough degrees of
1766 o An error message was sometimes issued by plot.multi.tree(),
1767 though with no consequence.
1771 CHANGES IN APE VERSION 1.8-1
1776 o There is a new plot method for lists of trees (objects of class
1777 "multi.tree"): it calls plot.phylo() internally and is
1778 documented on the same help page.
1783 o A bug was fixed in the C code that analyzes bipartitions: this
1784 has impact on several functions like prop.part, prop.clades,
1785 boot.phylo, or consensus.
1787 o root() did not work correctly when the specified outgroup had
1788 more than one element: this is fixed.
1790 o dist.dna() sometimes returned a warning inappropriately: this
1793 o If the distance object given to nj() had no rownames, nj()
1794 returned a tree with no tip labels: it now returns tips labelled
1795 "1", "2", ..., corresponding to the row numbers.
1800 o nj() has been slightly changed so that tips with a zero distance
1801 are first aggregated with zero-lengthed branches; the usual NJ
1802 procedure is then performed on a distance matrix without 0's.
1806 CHANGES IN APE VERSION 1.8
1811 o The new function chronopl() estimates dates using the penalized
1812 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1814 o The new function consensus() calculates the consensus tree of a
1817 o The new function evolve.phylo() simulates the evolution of
1818 continuous characters along a phylogeny under a Brownian model.
1820 o The new plot method for objects of class "ancestral" displays a
1821 tree together with ancestral values, as returned by the above
1824 o The new function as.phylo.formula() returns a phylogeny from a
1825 set of nested taxonomic variables given as a formula.
1827 o The new function read.caic() reads trees in CAIC format.
1829 o The new function tiplabels() allows to add labels to the tips
1830 of a tree using text or plotting symbols in a flexible way.
1832 o The new function unroot() unroots a phylogeny.
1834 o multi2di() has a new option, `random', which specifies whether
1835 to resolve the multichotomies randomly (the default) or not.
1837 o prop.part() now returns an object of class "prop.part" for which
1838 there are print (to display a partition in a more friendly way)
1839 and summary (to extract the numbers) methods.
1841 o plot.phylo() has a new option, `show.tip.label', specifying
1842 whether to print the labels of the tips. The default is TRUE.
1844 o The code of nj() has been replaced by a faster C code: it is now
1845 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1848 o write.nexus() now writes whether a tree is rooted or not.
1853 o Two bugs have been fixed in root(): unrooted trees are now
1854 handled corretly, and node labels are now output normally.
1856 o A bug was fixed in phymltest(): the executable couldn't be found
1859 o Three bug have been fixed in ace(): computing the likelihood of
1860 ancestral states of discrete characters failed, custom models
1861 did not work, and the function failed with a null gradient (a
1862 warning message is now returned; this latter bug was also
1863 present in yule.cov() as well and is now fixed).
1865 o pic() hanged out when missing data were present: a message error
1868 o A small bug was fixed in dist.dna() where the gamma correction
1869 was not always correctly dispatched.
1871 o plot.phylo() plotted correctly the root edge only when the tree
1872 was plotted rightwards: this works now for all directions.
1877 o dist.taxo() has been renamed as weight.taxo().
1879 o dist.phylo() has been replaced by the method cophenetic.phylo().
1881 o Various error and warning messages have been improved.
1885 CHANGES IN APE VERSION 1.7
1888 o The new function ace() estimates ancestral character states for
1889 continuous characters (with ML, GLS, and contrasts methods), and
1890 discrete characters (with ML only) for any number of states.
1892 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1893 of directional evolution for continuous characters. The user
1894 specifies the node(s) of the tree where the character optimum
1897 o The new function is.rooted() tests whether a tree (of class
1900 o The new function rcoal() generates random ultrametric trees with
1901 the possibility to specify the function that generates the
1902 inter-nodes distances.
1904 o The new function mrca() gives for all pairs of tips in a tree
1905 (and optionally nodes too) the most recent common ancestor.
1907 o nodelabels() has a new option `thermo' to plot proportions (up
1908 to three classes) on the nodes of a tree.
1910 o rtree() has been improved: it can now generate rooted or
1911 unrooted trees, and the mathematical function that generates the
1912 branch lengths may be specified by the user. The tip labels may
1913 be given directly in the call to rtree. The limit cases (n = 2,
1914 3) are now handled correctly.
1916 o dist.topo() has a new argument `method' with two choices: "PH85"
1917 for Penny and Henny's method (already available before and now
1918 the default), and "BHV01" for the geometric distance by Billera
1919 et al. (2001, Adv. Appl. Math. 27:733).
1921 o write.tree() has a new option, `digits', which specifies the
1922 number of digits to be printed in the Newick tree. By default
1923 digits = 10. The numbers are now always printed in decimal form
1924 (i.e., 1.0e-1 is now avoided).
1926 o dist.dna() can now compute the raw distances between pairs of
1927 DNA sequences by specifying model = "raw".
1929 o dist.phylo() has a new option `full' to possibly compute the
1930 distances among all tips and nodes of the tree. The default if
1936 o Several bugs were fixed in all.equal.phylo().
1938 o dist.dna() did not handle correctly gaps ("-") in alignments:
1939 they are now considered as missing data.
1941 o rotate() did not work if the tips were not ordered: this is
1944 o mantel.test() returned NA in some special cases: this is fixed
1945 and the function has been improved and is now faster.
1947 o A bug was fixed in diversi.gof() where the calculation of A² was
1950 o cherry() did not work correctly under some OSs (mainly Linux):
1953 o is.binary.tree() has been modified so that it works with both
1954 rooted and unrooted trees.
1956 o The documentation of theta.s() was not correct: this has been
1959 o plot.mst() did not work correctly: this is fixed.
1963 CHANGES IN APE VERSION 1.6
1968 o The new function dist.topo() computes the topological distances
1971 o The new function boot.phylo() performs a bootstrap analysis on
1972 phylogeny estimation.
1974 o The new functions prop.part() and prop.clades() analyse
1975 bipartitions from a series of trees.
1980 o read.GenBank() now uses the EFetch utility of NCBI instead of
1981 the usual Web interface: it is now much faster (e.g., 12 times
1982 faster to retrieve 8 sequences, 37 times for 60 sequences).
1987 o Several bugs were fixed in read.dna().
1989 o Several bugs were fixed in diversi.time().
1991 o is.binary.tree() did not work correctly if the tree has no edge
1992 lengths: this is fixed.
1994 o drop.tip() did not correctly propagated the `node.label' of a
1995 tree: this is fixed.
1999 CHANGES IN APE VERSION 1.5
2004 o Two new functions, as.matching.phylo() and as.phylo.matching(),
2005 convert objects between the classes "phylo" and "matching". The
2006 latter implements the representation of binary trees introduced by
2007 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
2008 as.matching() has been introduced as well.
2010 o Two new functions, multi2di() and di2multi(), allow to resolve
2011 and collapse multichotomies with branches of length zero.
2013 o The new function nuc.div() computes the nucleotide diversity
2014 from a sample a DNA sequences.
2016 o dist.dna() has been completely rewritten with a much faster
2017 (particularly for large data sets) C code. Eight models are
2018 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
2019 option `method' has been renamed `model'). Computation of variance
2020 is available for all models. A gamma-correction is possible for
2021 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
2022 to remove sites with missing data on a pairwise basis. The option
2023 `GCcontent' has been removed.
2025 o read.GenBank() has a new option (species.names) which specifies
2026 whether to return the species names of the organisms in addition
2027 to the accession numbers of the sequences (this is the default
2030 o write.nexus() can now write several trees in the same NEXUS file.
2032 o drop.tip() has a new option `root.edge' that allows to specify the
2033 new root edge if internal branches are trimmed.
2038 o as.phylo.hclust() failed if some labels had parentheses: this
2041 o Several bugs were fixed in all.equal.phylo(). This function now
2042 returns the logical TRUE if the trees are identical but with
2043 different representations (a report was printed previously).
2045 o read.GenBank() did not correctly handle ambiguous base codes:
2051 o birthdeath() now returns an object of class "birthdeath" for
2052 which there is a print method.
2056 CHANGES IN APE VERSION 1.4
2061 o The new function nj() performs phylogeny estimation with the
2062 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
2065 o The new function which.edge() identifies the edges of a tree
2066 that belong to a group specified as a set of tips.
2068 o The new function as.phylo.phylog() converts an object of class
2069 "phylog" (from the package ade4) into an object of class
2072 o The new function axisPhylo() draws axes on the side of a
2075 o The new function howmanytrees() calculates the number of trees
2076 in different cases and giving a number of tips.
2078 o write.tree() has a new option `multi.line' (TRUE by default) to
2079 write a Newick tree on several lines rather than on a single
2082 o The functionalities of zoom() have been extended. Several
2083 subtrees can be visualized at the same time, and they are marked
2084 on the main tree with colors. The context of the subtrees can be
2085 marked with the option `subtree' (see below).
2087 o drop.tip() has a new option `subtree' (FALSE by default) which
2088 specifies whether to output in the tree how many tips have been
2091 o The arguments of add.scale.bar() have been redefined and have
2092 now default values (see ?add.scale.bar for details). This
2093 function now works even if the plotted tree has no edge length.
2095 o plot.phylo() can now plot radial trees, but this does not take
2096 edge lengths into account.
2098 o In plot.phylo() with `type = "phylogram"', if the values of
2099 `edge.color' and `edge.width' are identical for sister-branches,
2100 they are propagated to the vertical line that link them.
2105 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
2106 crashing. This is fixed.
2108 o In plot.phylo(), the options `edge.color' and `edge.width' are
2109 now properly recycled; their default values are now "black" and
2112 o A bug has been fixed in write.nexus().
2117 o The function node.depth.edgelength() has been removed and
2118 replaced by a C code.
2122 CHANGES IN APE VERSION 1.3-1
2127 o The new function nodelabels() allows to add labels to the nodes
2128 of a tree using text or plotting symbols in a flexible way.
2130 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
2131 numeric values specifying the lower and upper limits on the x-
2132 and y-axes. This allows to leave some space on any side of the
2133 tree. If a single value is given, this is taken as the upper
2138 CHANGES IN APE VERSION 1.3
2143 o The new function phymltest() calls the software PHYML and fits
2144 28 models of DNA sequence evolution. There are a print method to
2145 display likelihood and AIC values, a summary method to compute
2146 the hierarchical likelihood ratio tests, and a plot method to
2147 display graphically the AIC values of each model.
2149 o The new function yule.cov() fits the Yule model with covariates,
2150 a model where the speciation rate is affected by several species
2151 traits through a generalized linear model. The parameters are
2152 estimated by maximum likelihood.
2154 o Three new functions, corBrownian(), corGrafen(), and
2155 corMartins(), compute the expected correlation structures among
2156 species given a phylogeny under different models of evolution.
2157 These can be used for GLS comparative phylogenetic methods (see
2158 the examples). There are coef() and corMatrix() methods and an
2159 Initialize.corPhyl() function associated.
2161 o The new function compar.cheverud() implements Cheverud et al.'s
2162 (1985; Evolution 39:1335) phylogenetic comparative method.
2164 o The new function varcomp() estimates variance components; it has
2167 o Two new functions, panel.superpose.correlogram() and
2168 plot.correlogramList(), allow to plot several phylogenetic
2171 o The new function node.leafnumber() computes the number of leaves
2172 of a subtree defined by a particular node.
2174 o The new function node.sons() gets all tags of son nodes from a
2177 o The new function compute.brlen() computes the branch lengths of
2178 a tree according to a specified method.
2180 o plot.phylo() has three new options: "cex" controls the size of
2181 the (tip and node) labels (thus it is no more needed to change
2182 the global graphical parameter), "direction" which allows to
2183 plot the tree rightwards, leftwards, upwards, or downwards, and
2184 "y.lim" which sets the upper limit on the y-axis.
2189 o Some functions which try to match tip labels and names of
2190 additional data (e.g. vector) are likely to fail if there are
2191 typing or syntax errors. If both series of names do not perfectly
2192 match, they are ignored and a warning message is now issued.
2193 These functions are bd.ext, compar.gee, pic. Their help pages
2194 have been clarified on this point.
2198 CHANGES IN APE VERSION 1.2-7
2203 o The new function root() reroots a phylogenetic tree with respect
2204 to a specified outgroup.
2206 o The new function rotate() rotates an internal branch of a tree.
2208 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
2209 trees) controls the display of the tip labels in unrooted trees.
2210 This display has been greatly improved: the tip labels are now not
2211 expected to overlap with the tree (particularly if lab4ut =
2212 "axial"). In all cases, combining appropriate values of "lab4ut"
2213 and the font size (via "par(cex = )") should result in readable
2214 unrooted trees. See ?plot.phylo for some examples.
2216 o In drop.tip(), the argument `tip' can now be numeric or character.
2221 o drop.tip() did not work correctly with trees with no branch
2222 lengths: this is fixed.
2224 o A bug in plot.phylo(..., type = "unrooted") made some trees being
2225 plotted with some line crossings: this is now fixed.
2229 CHANGES IN APE VERSION 1.2-6
2234 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
2235 correlogram.phylo, dist.taxo, plot.correlogram) have been added
2236 to implement comparative methods with an autocorrelation approach.
2238 o A new data set describing some life history traits of Carnivores
2244 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
2249 o When plotting a tree with plot.phylo(), the new default of the
2250 option `label.offset' is now 0, so the labels are always visible.
2254 CHANGES IN APE VERSION 1.2-5
2259 o The new function bd.ext() fits a birth-death model with combined
2260 phylogenetic and taxonomic data, and estimates the corresponding
2261 speciation and extinction rates.
2266 o The package gee is no more required by ape but only suggested
2267 since only the function compar.gee() calls gee.
2271 CHANGES IN APE VERSION 1.2-4
2276 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
2277 and lines.popsize) implementing a new approach for inferring the
2278 demographic history from genealogies using a reversible jump
2279 MCMC have been introduced.
2281 o The unit of time in the skyline plot and in the new plots can
2282 now be chosen to be actual years, rather than substitutions.
2286 CHANGES IN APE VERSION 1.2-3
2291 o The new function rtree() generates a random binary tree with or
2292 without branch lengths.
2294 o Two new functions for drawing lineages-through-time (LTT) plots
2295 are provided: ltt.lines() adds a LTT curve to an existing plot,
2296 and mltt.plot() does a multiple LTT plot giving several trees as
2297 arguments (see `?ltt.plot' for details).
2302 o Some taxon names made R crashing when calling as.phylo.hclust():
2305 o dist.dna() returned an error with two identical DNA sequences
2306 (only using the Jukes-Cantor method returned 0): this is fixed.
2311 o The function dist.phylo() has been re-written using a different
2312 algorithm: it is now about four times faster.
2314 o The code of branching.times() has been improved: it is now about
2319 CHANGES IN APE VERSION 1.2-2
2324 o The new function seg.sites() finds the segregating sites in a
2325 sample of DNA sequences.
2330 o A bug introduced in read.tree() and in read.nexus() with version
2333 o A few errors were corrected and a few examples were added in the
2338 CHANGES IN APE VERSION 1.2-1
2343 o plot.phylo() can now draw the edge of the root of a tree if it
2344 has one (see the new option `root.edge', its default is FALSE).
2349 o A bug was fixed in read.nexus(): files with semicolons inside
2350 comment blocks were not read correctly.
2352 o The behaviour of read.tree() and read.nexus() was corrected so
2353 that tree files with badly represented root edges (e.g., with
2354 an extra pair of parentheses, see the help pages for details)
2355 are now correctly represented in the object of class "phylo";
2356 a warning message is now issued.
2360 CHANGES IN APE VERSION 1.2
2365 o plot.phylo() has been completely re-written and offers several
2366 new functionalities. Three types of trees can now be drawn:
2367 phylogram (as previously), cladogram, and unrooted tree; in
2368 all three types the branch lengths can be drawn using the edge
2369 lengths of the phylogeny or not (e.g., if the latter is absent).
2370 The vertical position of the nodes can be adjusted with two
2371 choices (see option `node.pos'). The code has been re-structured,
2372 and two new functions (potentially useful for developpers) are
2373 documented separately: node.depth.edgelength() and node.depth();
2374 see the respective help pages for details.
2376 o The new function zoom() allows to explore very large trees by
2377 focusing on a small portion of it.
2379 o The new function yule() fits by maximum likelihood the Yule model
2380 (birth-only process) to a phylogenetic tree.
2382 o Support for writing DNA sequences in FASTA format has been
2383 introduced in write.dna() (support for reading sequences in
2384 this format was introduced in read.dna() in version 1.1-2).
2385 The function has been completely re-written, fixing some bugs
2386 (see below); the default behaviour is no more to display the
2387 sequences on the standard output. Several options have been
2388 introduced to control the sequence printing in a flexible
2389 way. The help page has been extended.
2391 o A new data set is included: a supertree of bats in NEXUS format.
2396 o In theta.s(), the default of the option `variance' has
2397 been changed to `FALSE' (as was indicated in the help page).
2399 o Several bugs were fixed in the code of all.equal.phylo().
2401 o Several bugs were fixed in write.dna(), particularly this
2402 function did not work with `format = "interleaved"'.
2404 o Various errors were corrected in the help pages.
2409 o The argument names of as.hclust.phylo() have been changed
2410 from "(phy)" to "(x, ...)" to conform to the definition of
2411 the corresponding generic function.
2413 o gamma.stat() has been renamed gammaStat() to avoid confusion
2414 since gamma() is a generic function.
2418 CHANGES IN APE VERSION 1.1-3
2423 o base.freq() previously did not return a value of 0 for
2424 bases absent in the data (e.g., a vector of length 3 was
2425 returned if one base was absent). This is now fixed (a
2426 vector of length 4 is always returned).
2428 o Several bugs were fixed in read.nexus(), including that this
2429 function did not work in this absence of a "TRANSLATE"
2430 command in the NEXUS file, and that the commands were
2435 CHANGES IN APE VERSION 1.1-2
2440 o The Tamura and Nei (1993) model of DNA distance is now implemented
2441 in dist.dna(): five models are now available in this function.
2443 o A new data set is included: a set of 15 sequences of the
2444 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2450 o A bug in read.nexus() was fixed.
2452 o read.dna() previously did not work correctly in most cases.
2453 The function has been completely re-written and its help page
2454 has been considerably extended (see ?read.dna for details).
2455 Underscores (_) in taxon names are no more replaced with
2456 spaces (this behaviour was undocumented).
2458 o A bug was fixed in write.dna().
2462 CHANGES IN APE VERSION 1.1-1
2467 o A bug in read.tree() introduced in APE 1.1 was fixed.
2469 o A bug in compar.gee() resulted in an error when trying to fit
2470 a model with `family = "binomial"'. This is now fixed.
2474 CHANGES IN APE VERSION 1.1
2479 o The Klastorin (1982) method as suggested by Misawa and Tajima
2480 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2481 on the basis of phylogenetic trees has been implemented (see
2482 the function klastorin()).
2484 o Functions have been added to convert APE's "phylo" objects in
2485 "hclust" cluster objects and vice versa (see the help page of
2486 as.phylo for details).
2488 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2489 are introduced for the estimation of absolute evolutionary rates
2490 (ratogram) and dated clock-like trees (chronogram) from
2491 phylogenetic trees using the non-parametric rate smoothing approach
2492 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2494 o A summary method is now provided printing a summary information on a
2495 phylogenetic tree with, for instance, `summary(tree)'.
2497 o The behaviour of read.tree() was changed so that all spaces and
2498 tabulations in tree files are now ignored. Consequently, spaces in tip
2499 labels are no more allowed. Another side effect is that read.nexus()
2500 now does not replace the underscores (_) in tip labels with spaces
2501 (this behaviour was undocumented).
2503 o The function plot.phylo() has a new option (`underscore') which
2504 specifies whether the underscores in tip labels should be written on
2505 the plot as such or replaced with spaces (the default).
2507 o The function birthdeath() now computes 95% confidence intervals of
2508 the estimated parameters using profile likelihood.
2510 o Three new data sets are included: a gene tree estimated from 36
2511 landplant rbcL sequences, a gene tree estimated from 32 opsin
2512 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2517 o A bug was fixed in dist.gene() where nothing was returned.
2519 o A bug in plot.mst() was fixed.
2521 o A bug in vcv.phylo() resulted in false correlations when the
2522 option `cor = TRUE' was used (now fixed).
2526 CHANGES IN APE VERSION 1.0
2531 o Two new functions, read.dna() and write.dna(), read/write in a file
2532 DNA sequences in interleaved or in sequential format.
2534 o Two new functions, read.nexus() and write.nexus(), read/write trees
2537 o The new function bind.tree() allows to bind two trees together,
2538 possibly handling root edges to give internal branches.
2540 o The new function drop.tip() removes the tips in a phylogenetic tree,
2541 and trims (or not) the corresponding internal branches.
2543 o The new function is.ultrametric() tests if a tree is ultrametric.
2545 o The function plot.phylo() has more functionalities such as drawing the
2546 branches with different colours and/or different widths, showing the
2547 node labels, controling the position and font of the labels, rotating
2548 the labels, and controling the space around the plot.
2550 o The function read.tree() can now read trees with no branch length,
2551 such as "(a,b),c);". Consequently, the element `edge.length' in
2552 objects of class "phylo" is now optional.
2554 o The function write.tree() has a new default behaviour: if the default
2555 for the option `file' is used (i.e. file = ""), then a variable of
2556 mode character containing the tree in Newick format is returned which
2557 can thus be assigned (e.g., tree <- write.tree(phy)).
2559 o The function read.tree() has a new argument `text' which allows
2560 to read the tree in a variable of mode character.
2562 o A new data set is included: the phylogenetic relationships among
2563 the orders of birds from Sibley and Ahlquist (1990).
2567 CHANGES IN APE VERSION 0.2-1
2572 o Several bugs were fixed in the help pages.
2576 CHANGES IN APE VERSION 0.2
2581 o The function write.tree() writes phylogenetic trees (objects of class
2582 "phylo") in an ASCII file using the Newick parenthetic format.
2584 o The function birthdeath() fits a birth-death model to branching times
2585 by maximum likelihood, and estimates the corresponding speciation and
2588 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2591 o The function is.binary.tree() tests whether a phylogeny is binary.
2593 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2594 as well as some methods are introduced.
2596 o Several functions, including some generics and methods, for computing
2597 skyline plot estimates (classic and generalized) of effective
2598 population size through time are introduced and replace the function
2599 skyline.plot() in version 0.1.
2601 o Two data sets are now included: the phylogenetic relationships among
2602 the families of birds from Sibley and Ahlquist (1990), and an
2603 estimated clock-like phylogeny of HIV sequences sampled in the
2604 Democratic Republic of Congo.
2607 DEPRECATED & DEFUNCT
2609 o The function skyline.plot() in ape 0.1 has been deprecated and
2610 replaced by more elaborate functions (see above).
2615 o Two important bugs were fixed in plot.phylo(): phylogenies with
2616 multichotomies not at the root or not with only terminal branches,
2617 and phylogenies with a single node (i.e. only terminal branches)
2618 did not plot. These trees should be plotted correctly now.
2620 o Several bugs were fixed in diversi.time() in the computation of
2623 o Various errors were corrected in the help pages.