1 CHANGES IN APE VERSION 2.2-3
6 o chronopl() did not work with CV = TRUE.
10 CHANGES IN APE VERSION 2.2-2
15 o dist.gene() has been substantially improved and gains an option
18 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
24 o prop.part() failed with a single tree with the default option
25 'check.labels = TRUE'.
27 o summary.DNAbin() failed to display correctly the summary of
28 sequence lengths with lists of sequences of 10,000 bases or more
29 (because summary.default uses 4 significant digits by default).
31 o read.nexus() failed to read a file with a single tree with line
32 breaks in the Newick string.
34 o del.gaps() returned a list of empty sequences when there were no
40 o phymltest() has been updated for PhyML 3.0 and gains an option
41 'append', whereas the option 'path2exec' has been removed.
43 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
44 which is returned unchanged (instead of an error).
46 o The data sets bird.orders and bird.families are now stored as
47 Newick strings; i.e., the command data(bird.orders) calls
52 CHANGES IN APE VERSION 2.2-1
57 o The new function makeLabel() helps to modify labels of trees,
58 lists of trees, or DNA sequences, with several utilities to
59 truncate and/or make them unique, substituting some
60 characters, and so on.
62 o The new function del.gaps() removes insertion gaps ("-") in a
65 o read.dna() can now read Clustal files (*.aln).
70 o root() failed with 'resolve.root = TRUE' when the root was
71 already the specified root.
73 o Several bugs were fixed in mlphylo().
75 o collapsed.singles() did not propagate the 'Nnode' and
76 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
78 o read.nexus() failed to remove correctly the comments within
81 o read.nexus() failed to read a file with a single tree and no
82 translation of tip labels.
84 o read.nexus() failed to place correctly tip labels when reading
85 a single tree with no edge lengths.
87 o A bug was fixed in sh.test().
92 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
95 o The option 'check.labels' of consensus() and prop.part() is now
98 o write.dna() now does not truncate names to 10 characters with
103 CHANGES IN APE VERSION 2.2
108 o Four new functions have been written by Damien de Vienne for the
109 graphical exploration of large trees (cophyloplot, subtrees,
110 subtreeplot), and to return the graphical coordinates of tree
113 o The new functions corPagel and corBlomberg implement the Pagel's
114 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
116 o chronopl() has been improved and gains several options: see its
117 help page for details.
119 o boot.phylo() has now an option 'trees' to possibly return the
120 bootstraped trees (the default is FALSE).
122 o prop.part() has been improved and should now be faster in all
128 o read.dna() failed if "?" occurred in the first 10 sites of the
131 o The x/y aspect of the plot is now respected when plotting a
132 circular tree (type = "r" or "f").
134 o Drawing the tip labels sometimes failed when plotting circular
137 o zoom() failed when tip labels were used instead of their numbers
138 (thanks to Yan Wong for the fix).
140 o drop.tip() failed with some trees (fixed by Yan Wong).
142 o seg.sites() failed with a list.
144 o consensus() failed in some cases. The function has been improved
145 as well and is faster.
149 CHANGES IN APE VERSION 2.1-3
154 o A bug in read.nexus() made the Windows R-GUI crash.
156 o An error was fixed in the computation of ancestral character
157 states by generalized least squares in ace().
159 o di2multi() did not modify node labels correctly.
161 o multi2di() failed if the tree had its attribute "order" set to
166 CHANGES IN APE VERSION 2.1-2
171 o There three new methods for the "multiPhylo" class: str, $,
174 o root() gains the options 'node' and 'resolve.root'
175 (FALSE by default) as well as its code being improved.
177 o mltt.plot() has now an option 'log' used in the same way
178 than in plot.default().
183 o mltt.plot() failed to display the legend with an unnamed
186 o nodelabels() with pies now correcly uses the argument
187 'cex' to draw symbols of different sizes (which has
188 worked already for thermometers).
190 o read.nexus() generally failed to read very big files.
195 o The argument 'family' of compar.gee() can now be a function
196 as well as a character string.
198 o read.tree() and read.nexus() now return an unnamed list if
201 o read.nexus() now returns a modified object of class "multiPhylo"
202 when there is a TRANSLATE block in the NEXUS file: the individual
203 trees have no 'tip.label' vector, but the list has a 'TipLabel'
204 attribute. The new methods '$' and '[[' set these elements
205 correctly when extracting trees.
209 CHANGES IN APE VERSION 2.1-1
214 o The new function rmtree generates lists of random trees.
216 o rcoal() now generates a genuine coalescent tree by default
217 (thanks to Vladimir Minin for the code).
222 o nuc.div() returned an incorrect value with the default
223 pairwise.deletion = FALSE.
228 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
229 have been improved so that they are stabler and faster.
231 o R packages used by ape are now loaded silently; lattice and gee
232 are loaded only when needed.
236 CHANGES IN APE VERSION 2.1
241 o The new function identify.phylo identifies clades on a plotted
242 tree using the mouse.
244 o It is now possible to subset a list of trees (object of class
245 "multiPhylo") with "[" while keeping its class correct.
247 o The new function as.DNAbin.alignment converts DNA sequences
248 stored in the "alignment" format of the package seqinr into
249 an object of class "DNAbin".
251 o The new function weight.taxo2 helps to build similarity matrices
252 given two taxonomic levels (usually called by other functions).
254 o write.tree() can now take a list of trees (class "multiPhylo")
255 as its main argument.
257 o plot.correlogram() and plot.correlogramList() have been
258 improved, and gain several options (see the help page for
259 details). A legend is now plotted by default.
264 o dist.dna() returned some incorrect values with `model = "JC69"'
265 and `pairwise.deletion = TRUE'. This affected only the
266 distances involving sequences with missing values. (Thanks
267 to Bruno Toupance for digging this bug out.)
269 o write.tree() failed with some trees: this is fixed by removing
270 the `multi.line' option (trees are now always printed on a
273 o read.nexus() did not correctly detect trees with multiple root
274 edges (see OTHER CHANGES).
279 o The code of mlphylo() has been almost entirely rewritten, and
280 should be much stabler. The options have been also greatly
281 simplified (see ?mlphylo and ?DNAmodel for details).
283 o The internal function nTips has been renamed klastorin_nTips.
285 o The code of is.ultrametric() contained redundancies and has
288 o The code of Moran.I() and of correlogram.formula() have been
291 o read.tree() and read.nexus() now return an error when trying to
292 read a tree with multiple root edges (see BUG FIXES). The
293 correction applied in previous version did not work in all
296 o The class c("multi.tree", "phylo") has been renamed
302 o There is now a vignette in ape: see vignette("MoranI", "ape").
307 o as.matching() and as.phylo.matching() do not support branch
310 o correlogram.phylo() and discrete.dist() have been removed.
314 CHANGES IN APE VERSION 2.0-2
319 o The new function matexpo computes the exponential of a square
322 o The new function unique.multi.tree removes duplicate trees from
325 o yule() has a new option `use.root.edge = FALSE' that specifies
326 to ignore, by default, the root edge of the tree if it exists.
331 o which.edge() failed when the index of a single terminal edge was
334 o In diversi.time(), the values returned for model C were
337 o A bug was fixed in yule() that affected the calculation of the
338 likelihood in the presence of ties in the branching times.
340 o There was a bug in the C function mat_expo4x4 affecting the
341 calculations of the transition probabilities for models HKY and
344 o A small bug was fixed in as.matrix.DNAbin (thanks to James
347 o rtree() did not `shuffle' the tip labels by default, so only a
348 limited number of labelled topologies could be generated.
352 CHANGES IN APE VERSION 2.0-1
357 o The three new functions bionj, fastme.ols, and fastme.bal
358 perform phylogeny estimation by the BIONJ and fastME methods in
359 OLS and balanced versions. This is a port to R of previous
360 previous programs done by Vincent Lefort.
362 o The new function chronoMPL performs molecular dating with the
363 mean path lengths method of Britton et al. (2002, Mol. Phyl.
366 o The new function rotate, contributed by Christoph Heibl, swaps
367 two clades connected to the same node. It works also with
368 multichotomous nodes.
370 o The new `method' as.matrix.DNAbin() may be used to convert
371 easily DNA sequences stored in a list into a matrix while
372 keeping the names and the class.
377 o chronopl() failed when some branch lengths were equal to zero:
378 an error message is now returned.
380 o di2multi() failed when there was a series of consecutive edges
385 CHANGES IN APE VERSION 1.10-2
390 o plot.phylo() can now plot circular trees: the option is type =
391 "fan" or type = "f" (to avoid the ambiguity with type = "c").
393 o prop.part() has a new option `check.labels = FALSE' which allows
394 to considerably speed-up the calculations of bipartitions. As a
395 consequence, calculations of bootstrap values with boot.phylo()
396 should be much faster.
401 o read.GenBank() did not return correctly the list of species as
402 from ape 1.10: this is fixed in this version
404 o Applying as.phylo() on a tree of class "phylo" failed: the
405 object is now returned unchanged.
409 CHANGES IN APE VERSION 1.10-1
414 o The three new functions Ntip, Nnode, and Nedge return, for a
415 given tree, the number of tips, nodes, or edges, respectively.
420 o read.nexus() did not set correctly the class of the returned
421 object when reading multiple trees.
423 o mllt.plot() failed with objects of class c("multi.tree",
426 o unroot() did not work correctly in most cases.
428 o reorder.phylo() made R freeze in some occasions.
430 o Plotting a tree in pruningwise order failed.
432 o When plotting an unrooted tree, the tip labels where not all
433 correctly positioned if the option `cex' was used.
437 CHANGES IN APE VERSION 1.10
442 o Five new `method' functions have been introduced to manipulate
443 DNA sequences in binary format (see below).
445 o Three new functions have been introduced to convert between the
446 new binary and the character formats.
448 o The new function as.alignment converts DNA sequences stored as
449 single characters into the class "alignment" used by the package
452 o read.dna() and read.GenBank() have a new argument `as.character'
453 controlling whether the sequences are returned in binary format
459 o root() failed when the tree had node labels: this is fixed.
461 o plot.phylo() did not correctly set the limits on the y-axis with
462 the default setting: this is fixed.
464 o dist.dna() returned a wrong result for the LogDet, paralinear,
465 and BH87 models with `pairwise.deletion = TRUE'.
470 o DNA sequences are now internally stored in a binary format. See
471 the document "A Bit-Level Coding Scheme for Nucleotides" for the
472 details. Most functions analyzing DNA functions have been
473 modified accordingly and are now much faster (dist.dna is now
474 ca. 60 times faster).
478 CHANGES IN APE VERSION 1.9-4
483 o A bug was fixed in edgelabels().
485 o as.phylo.hclust() did not work correctly when the object of
486 class "hclust" has its labels set to NULL: the returned tree has
487 now its tip labels set to "1", "2", ...
489 o consensus could fail if some tip labels are a subset of others
490 (e.g., "a" and "a_1"): this is now fixed.
492 o mlphylo() failed in most cases if some branch lengths of the
493 initial tree were greater than one: an error message is now
496 o mlphylo() failed in most cases when estimating the proportion of
497 invariants: this is fixed.
501 CHANGES IN APE VERSION 1.9-3
506 o The new function edgelabels adds labels on the edge of the tree
507 in the same way than nodelabels or tiplabels.
512 o multi2di() did not handle correctly branch lengths with the
513 default option `random = TRUE': this is now fixed.
515 o A bug was fixed in nuc.div() when using pairwise deletions.
517 o A bug occurred in the analysis of bipartitions with large
518 numbers of large trees, with consequences on prop.part,
519 prop.clades, and boot.phylo.
521 o The calculation of the Billera-Holmes-Vogtmann distance in
522 dist.topo was wrong: this has been fixed.
526 CHANGES IN APE VERSION 1.9-2
531 o The new function ladderize reorganizes the internal structure of
532 a tree to plot them left- or right-ladderized.
534 o The new function dist.nodes computes the patristic distances
535 between all nodes, internal and terminal, of a tree. It replaces
536 the option `full = TRUE' of cophenetic.phylo (see below).
541 o A bug was fixed in old2new.phylo().
543 o Some bugs were fixed in chronopl().
545 o The edge colours were not correctly displayed by plot.phylo
546 (thank you to Li-San Wang for the fix).
548 o cophenetic.phylo() failed with multichotomous trees: this is
554 o read.dna() now returns the sequences in a matrix if they are
555 aligned (interleaved or sequential format). Sequences in FASTA
556 format are still returned in a list.
558 o The option `full' of cophenetic.phylo() has been removed because
559 it could not be used from the generic.
564 o rotate() has been removed; this function did not work correctly
569 CHANGES IN APE VERSION 1.9-1
574 o Trees with a single tip were not read correctly in R as the
575 element `Nnode' was not set: this is fixed.
577 o unroot() did not set correctly the number of nodes of the
578 unrooted tree in most cases.
580 o read.GenBank() failed when fetching very long sequences,
581 particularly of the BX-series.
583 o A bug was introduced in read.tree() with ape 1.9: it has been
588 CHANGES IN APE VERSION 1.9
593 o There are two new print `methods' for trees of class "phylo" and
594 lists of trees of class "multi.tree", so that they are now
595 displayed in a compact and informative way.
597 o There are two new functions, old2new.phylo and new2old.phylo,
598 for converting between the old and new coding of the class
601 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
602 LogDet ("logdet"), and paralinear ("paralin").
604 o compute.brlen() has been extended: several methods are now
605 available to compute branch lengths.
607 o write.dna() can now handle matrices as well as lists.
612 o cophenetic.phylo() sometimes returned a wrong result with
613 multichotomous trees: this is fixed.
615 o rotate() failed when a single tip was specified: the tree is now
618 o ace() did not return the correct index matrix with custom
619 models: this is fixed.
621 o multi2di() did not work correctly when resolving multichotomies
622 randomly: the topology was always the same, only the arrangement
623 of clades was randomized: this is fixed. This function now
624 accepts trees with no branch lengths.
626 o The output of diversi.gof() was blurred by useless prints when a
627 user distribution was specified. This has been corrected, and
628 the help page of this function has been expanded.
633 o The internal structure of the class "phylo" has been changed:
634 see the document "Definition of Formats for Coding Phylogenetic
635 Trees in R" for the details. In addition, the code of most
636 functions has been improved.
638 o Several functions have been improved by replacing some R codes
639 by C codes: pic, plot.phylo, and reorder.phylo.
641 o There is now a citation information: see citation("ape") in R.
643 o write.tree() now does not add extra 0's to branch lengths so
644 that 1.23 is printed "1.23" by default, not "1.2300000000".
646 o The syntax of bind.tree() has been simplified. This function now
647 accepts trees with no branch lengths, and handles correctly node
650 o The option `as.numeric' of mrca() has been removed.
652 o The unused options `format' and `rooted' of read.tree() have
655 o The unused option `format' of write.tree() has been removed.
657 o The use of node.depth() has been simplified.
661 CHANGES IN APE VERSION 1.8-5
666 o Two new functions read.nexus.data() and write.nexus.data(),
667 contributed by Johan Nylander, allow to read and write molecular
668 sequences in NEXUS files.
670 o The new function reorder.phylo() reorders the internal structure
671 of a tree of class "phylo". It is used as the generic, e.g.,
674 o read.tree() and read.nexus() can now read trees with a single
677 o The new data set `cynipids' supplies a set of protein sequences
683 o The code of all.equal.phylo() has been completely rewritten
684 (thanks to Benoît Durand) which fixes several bugs.
686 o read.tree() and read.nexus() now checks the labels of the tree
687 to remove or substitute any characters that are illegal in the
688 Newick format (parentheses, etc.)
690 o A negative P-value could be returned by mantel.test(): this is
695 CHANGES IN APE VERSION 1.8-4
700 o The new function sh.test() computes the Shimodaira-
703 o The new function collapse.singles() removes the nodes with a
704 single descendant from a tree.
706 o plot.phylo() has a new argument `tip.color' to specify the
709 o mlphylo() has now an option `quiet' to control the display of
710 the progress of the analysis (the default is FALSE).
715 o read.dna() did not read correctly sequences in sequential format
716 with leading alignment gaps "-": this is fixed.
718 o ace() returned a list with no class so that the generic
719 functions (anova, logLik, ...) could not be used directly. This
720 is fixed as ace() now returns an object of class "ace".
722 o anova.ace() had a small bug when computing the number of degrees
723 of freedom: this is fixed.
725 o mlphylo() did not work when the sequences were in a matrix or
726 a data frame: this is fixed.
728 o rtree() did not work correctly when trying to simulate an
729 unrooted tree with two tips: an error message is now issued.
734 o The algorithm of rtree() has been changed: it is now about 40,
735 100, and 130 times faster for 10, 100, and 1000 tips,
740 CHANGES IN APE VERSION 1.8-3
745 o There are four new `method' functions to be used with the
746 results of ace(): logLik(), deviance(), AIC(), and anova().
748 o The plot method of phymltest has two new arguments: `main' to
749 change the title, and `col' to control the colour of the
750 segments showing the AIC values.
752 o ace() has a new argument `ip' that gives the initial values used
753 in the ML estimation with discrete characters (see the examples
754 in ?ace). This function now returns a matrix giving the indices
755 of the estimated rates when analysing discrete characters.
757 o nodelabels() and tiplabels() have a new argument `pie' to
758 represent proportions, with any number of categories, as
759 piecharts. The use of the option `thermo' has been improved:
760 there is now no limitation on the number of categories.
765 o mlphylo() did not work with more than two partitions: this is
768 o root() failed if the proposed outgroup was already an outgroup
769 in the tree: this is fixed.
771 o The `col' argument in nodelabels() and tiplabels() was not
772 correctly passed when `text' was used: this is fixed.
774 o Two bugs were fixed in mlphylo(): parameters were not always
775 correctly output, and the estimation failed in some cases.
777 o plot.phylo() was stuck when given a tree with a single tip: this
778 is fixed and a message error is now returned.
780 o An error was corrected in the help page of gammaStat regarding
781 the calculation of P-values.
783 o Using gls() could crash R when the number of species in the tree
784 and in the variables were different: this is fixed.
788 CHANGES IN APE VERSION 1.8-2
793 o The new function mlphylo() fits a phylogenetic tree by maximum
794 likelihood from DNA sequences. Its companion function DNAmodel()
795 is used to define the substitution model which may include
796 partitioning. There are methods for logLik(), deviance(), and
797 AIC(), and the summary() method has been extended to display in
798 a friendly way the results of this model fitting. Currently, the
799 functionality is limited to estimating the substitution and
800 associated parameters and computing the likelihood.
802 o The new function drop1.compar.gee (used as, e.g., drop1(m))
803 tests for single effects in GEE-based comparative method. A
804 warning message is printed if there is not enough degrees of
810 o An error message was sometimes issued by plot.multi.tree(),
811 though with no consequence.
815 CHANGES IN APE VERSION 1.8-1
820 o There is a new plot method for lists of trees (objects of class
821 "multi.tree"): it calls plot.phylo() internally and is
822 documented on the same help page.
827 o A bug was fixed in the C code that analyzes bipartitions: this
828 has impact on several functions like prop.part, prop.clades,
829 boot.phylo, or consensus.
831 o root() did not work correctly when the specified outgroup had
832 more than one element: this is fixed.
834 o dist.dna() sometimes returned a warning inappropriately: this
837 o If the distance object given to nj() had no rownames, nj()
838 returned a tree with no tip labels: it now returns tips labelled
839 "1", "2", ..., corresponding to the row numbers.
844 o nj() has been slightly changed so that tips with a zero distance
845 are first aggregated with zero-lengthed branches; the usual NJ
846 procedure is then performed on a distance matrix without 0's.
850 CHANGES IN APE VERSION 1.8
855 o The new function chronopl() estimates dates using the penalized
856 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
858 o The new function consensus() calculates the consensus tree of a
861 o The new function evolve.phylo() simulates the evolution of
862 continuous characters along a phylogeny under a Brownian model.
864 o The new plot method for objects of class "ancestral" displays a
865 tree together with ancestral values, as returned by the above
868 o The new function as.phylo.formula() returns a phylogeny from a
869 set of nested taxonomic variables given as a formula.
871 o The new function read.caic() reads trees in CAIC format.
873 o The new function tiplabels() allows to add labels to the tips
874 of a tree using text or plotting symbols in a flexible way.
876 o The new function unroot() unroots a phylogeny.
878 o multi2di() has a new option, `random', which specifies whether
879 to resolve the multichotomies randomly (the default) or not.
881 o prop.part() now returns an object of class "prop.part" for which
882 there are print (to display a partition in a more friendly way)
883 and summary (to extract the numbers) methods.
885 o plot.phylo() has a new option, `show.tip.label', specifying
886 whether to print the labels of the tips. The default is TRUE.
888 o The code of nj() has been replaced by a faster C code: it is now
889 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
892 o write.nexus() now writes whether a tree is rooted or not.
897 o Two bugs have been fixed in root(): unrooted trees are now
898 handled corretly, and node labels are now output normally.
900 o A bug was fixed in phymltest(): the executable couldn't be found
903 o Three bug have been fixed in ace(): computing the likelihood of
904 ancestral states of discrete characters failed, custom models
905 did not work, and the function failed with a null gradient (a
906 warning message is now returned; this latter bug was also
907 present in yule.cov() as well and is now fixed).
909 o pic() hanged out when missing data were present: a message error
912 o A small bug was fixed in dist.dna() where the gamma correction
913 was not always correctly dispatched.
915 o plot.phylo() plotted correctly the root edge only when the tree
916 was plotted rightwards: this works now for all directions.
921 o dist.taxo() has been renamed as weight.taxo().
923 o Various error and warning messages have been improved.
927 CHANGES IN APE VERSION 1.7
930 o The new function ace() estimates ancestral character states for
931 continuous characters (with ML, GLS, and contrasts methods), and
932 discrete characters (with ML only) for any number of states.
934 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
935 of directional evolution for continuous characters. The user
936 specifies the node(s) of the tree where the character optimum
939 o The new function is.rooted() tests whether a tree (of class
942 o The new function rcoal() generates random ultrametric trees with
943 the possibility to specify the function that generates the
944 inter-nodes distances.
946 o The new function mrca() gives for all pairs of tips in a tree
947 (and optionally nodes too) the most recent common ancestor.
949 o nodelabels() has a new option `thermo' to plot proportions (up
950 to three classes) on the nodes of a tree.
952 o rtree() has been improved: it can now generate rooted or
953 unrooted trees, and the mathematical function that generates the
954 branch lengths may be specified by the user. The tip labels may
955 be given directly in the call to rtree. The limit cases (n = 2,
956 3) are now handled correctly.
958 o dist.topo() has a new argument `method' with two choices: "PH85"
959 for Penny and Henny's method (already available before and now
960 the default), and "BHV01" for the geometric distance by Billera
961 et al. (2001, Adv. Appl. Math. 27:733).
963 o write.tree() has a new option, `digits', which specifies the
964 number of digits to be printed in the Newick tree. By default
965 digits = 10. The numbers are now always printed in decimal form
966 (i.e., 1.0e-1 is now avoided).
968 o dist.dna() can now compute the raw distances between pairs of
969 DNA sequences by specifying model = "raw".
971 o dist.phylo() has a new option `full' to possibly compute the
972 distances among all tips and nodes of the tree. The default if
978 o Several bugs were fixed in all.equal.phylo().
980 o dist.dna() did not handle correctly gaps ("-") in alignments:
981 they are now considered as missing data.
983 o rotate() did not work if the tips were not ordered: this is
986 o mantel.test() returned NA in some special cases: this is fixed
987 and the function has been improved and is now faster.
989 o A bug was fixed in diversi.gof() where the calculation of A² was
992 o cherry() did not work correctly under some OSs (mainly Linux):
995 o is.binary.tree() has been modified so that it works with both
996 rooted and unrooted trees.
998 o The documentation of theta.s() was not correct: this has been
1001 o plot.mst() did not work correctly: this is fixed.
1005 CHANGES IN APE VERSION 1.6
1010 o The new function dist.topo() computes the topological distances
1013 o The new function boot.phylo() performs a bootstrap analysis on
1014 phylogeny estimation.
1016 o The new functions prop.part() and prop.clades() analyse
1017 bipartitions from a series of trees.
1022 o read.GenBank() now uses the EFetch utility of NCBI instead of
1023 the usual Web interface: it is now much faster (e.g., 12 times
1024 faster to retrieve 8 sequences, 37 times for 60 sequences).
1029 o Several bugs were fixed in read.dna().
1031 o Several bugs were fixed in diversi.time().
1033 o is.binary.tree() did not work correctly if the tree has no edge
1034 lengths: this is fixed.
1036 o drop.tip() did not correctly propagated the `node.label' of a
1037 tree: this is fixed.
1041 CHANGES IN APE VERSION 1.5
1046 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1047 convert objects between the classes "phylo" and "matching". The
1048 latter implements the representation of binary trees introduced by
1049 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1050 as.matching() has been introduced as well.
1052 o Two new functions, multi2di() and di2multi(), allow to resolve
1053 and collapse multichotomies with branches of length zero.
1055 o The new function nuc.div() computes the nucleotide diversity
1056 from a sample a DNA sequences.
1058 o dist.dna() has been completely rewritten with a much faster
1059 (particularly for large data sets) C code. Eight models are
1060 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1061 option `method' has been renamed `model'). Computation of variance
1062 is available for all models. A gamma-correction is possible for
1063 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1064 to remove sites with missing data on a pairwise basis. The option
1065 `GCcontent' has been removed.
1067 o read.GenBank() has a new option (species.names) which specifies
1068 whether to return the species names of the organisms in addition
1069 to the accession numbers of the sequences (this is the default
1072 o write.nexus() can now write several trees in the same NEXUS file.
1074 o drop.tip() has a new option `root.edge' that allows to specify the
1075 new root edge if internal branches are trimmed.
1080 o as.phylo.hclust() failed if some labels had parentheses: this
1083 o Several bugs were fixed in all.equal.phylo(). This function now
1084 returns the logical TRUE if the trees are identical but with
1085 different representations (a report was printed previously).
1087 o read.GenBank() did not correctly handle ambiguous base codes:
1093 o birthdeath() now returns an object of class "birthdeath" for
1094 which there is a print method.
1098 CHANGES IN APE VERSION 1.4
1103 o The new function nj() performs phylogeny estimation with the
1104 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1107 o The new function which.edge() identifies the edges of a tree
1108 that belong to a group specified as a set of tips.
1110 o The new function as.phylo.phylog() converts an object of class
1111 "phylog" (from the package ade4) into an object of class
1114 o The new function axisPhylo() draws axes on the side of a
1117 o The new function howmanytrees() calculates the number of trees
1118 in different cases and giving a number of tips.
1120 o write.tree() has a new option `multi.line' (TRUE by default) to
1121 write a Newick tree on several lines rather than on a single
1124 o The functionalities of zoom() have been extended. Several
1125 subtrees can be visualized at the same time, and they are marked
1126 on the main tree with colors. The context of the subtrees can be
1127 marked with the option `subtree' (see below).
1129 o drop.tip() has a new option `subtree' (FALSE by default) which
1130 specifies whether to output in the tree how many tips have been
1133 o The arguments of add.scale.bar() have been redefined and have
1134 now default values (see ?add.scale.bar for details). This
1135 function now works even if the plotted tree has no edge length.
1137 o plot.phylo() can now plot radial trees, but this does not take
1138 edge lengths into account.
1140 o In plot.phylo() with `type = "phylogram"', if the values of
1141 `edge.color' and `edge.width' are identical for sister-branches,
1142 they are propagated to the vertical line that link them.
1147 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1148 crashing. This is fixed.
1150 o In plot.phylo(), the options `edge.color' and `edge.width' are
1151 now properly recycled; their default values are now "black" and
1154 o A bug has been fixed in write.nexus().
1159 o The function node.depth.edgelength() has been removed and
1160 replaced by a C code.
1164 CHANGES IN APE VERSION 1.3-1
1169 o The new function nodelabels() allows to add labels to the nodes
1170 of a tree using text or plotting symbols in a flexible way.
1172 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1173 numeric values specifying the lower and upper limits on the x-
1174 and y-axes. This allows to leave some space on any side of the
1175 tree. If a single value is given, this is taken as the upper
1180 CHANGES IN APE VERSION 1.3
1185 o The new function phymltest() calls the software PHYML and fits
1186 28 models of DNA sequence evolution. There are a print method to
1187 display likelihood and AIC values, a summary method to compute
1188 the hierarchical likelihood ratio tests, and a plot method to
1189 display graphically the AIC values of each model.
1191 o The new function yule.cov() fits the Yule model with covariates,
1192 a model where the speciation rate is affected by several species
1193 traits through a generalized linear model. The parameters are
1194 estimated by maximum likelihood.
1196 o Three new functions, corBrownian(), corGrafen(), and
1197 corMartins(), compute the expected correlation structures among
1198 species given a phylogeny under different models of evolution.
1199 These can be used for GLS comparative phylogenetic methods (see
1200 the examples). There are coef() and corMatrix() methods and an
1201 Initialize.corPhyl() function associated.
1203 o The new function compar.cheverud() implements Cheverud et al.'s
1204 (1985; Evolution 39:1335) phylogenetic comparative method.
1206 o The new function varcomp() estimates variance components; it has
1209 o Two new functions, panel.superpose.correlogram() and
1210 plot.correlogramList(), allow to plot several phylogenetic
1213 o The new function node.leafnumber() computes the number of leaves
1214 of a subtree defined by a particular node.
1216 o The new function node.sons() gets all tags of son nodes from a
1219 o The new function compute.brlen() computes the branch lengths of
1220 a tree according to a specified method.
1222 o plot.phylo() has three new options: "cex" controls the size of
1223 the (tip and node) labels (thus it is no more needed to change
1224 the global graphical parameter), "direction" which allows to
1225 plot the tree rightwards, leftwards, upwards, or downwards, and
1226 "y.lim" which sets the upper limit on the y-axis.
1231 o Some functions which try to match tip labels and names of
1232 additional data (e.g. vector) are likely to fail if there are
1233 typing or syntax errors. If both series of names do not perfectly
1234 match, they are ignored and a warning message is now issued.
1235 These functions are bd.ext, compar.gee, pic. Their help pages
1236 have been clarified on this point.
1240 CHANGES IN APE VERSION 1.2-7
1245 o The new function root() reroots a phylogenetic tree with respect
1246 to a specified outgroup.
1248 o The new function rotate() rotates an internal branch of a tree.
1250 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1251 trees) controls the display of the tip labels in unrooted trees.
1252 This display has been greatly improved: the tip labels are now not
1253 expected to overlap with the tree (particularly if lab4ut =
1254 "axial"). In all cases, combining appropriate values of "lab4ut"
1255 and the font size (via "par(cex = )") should result in readable
1256 unrooted trees. See ?plot.phylo for some examples.
1258 o In drop.tip(), the argument `tip' can now be numeric or character.
1263 o drop.tip() did not work correctly with trees with no branch
1264 lengths: this is fixed.
1266 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1267 plotted with some line crossings: this is now fixed.
1271 CHANGES IN APE VERSION 1.2-6
1276 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1277 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1278 to implement comparative methods with an autocorrelation approach.
1280 o A new data set describing some life history traits of Carnivores
1286 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1291 o When plotting a tree with plot.phylo(), the new default of the
1292 option `label.offset' is now 0, so the labels are always visible.
1296 CHANGES IN APE VERSION 1.2-5
1301 o The new function bd.ext() fits a birth-death model with combined
1302 phylogenetic and taxonomic data, and estimates the corresponding
1303 speciation and extinction rates.
1308 o The package gee is no more required by ape but only suggested
1309 since only the function compar.gee() calls gee.
1313 CHANGES IN APE VERSION 1.2-4
1318 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1319 and lines.popsize) implementing a new approach for inferring the
1320 demographic history from genealogies using a reversible jump
1321 MCMC have been introduced.
1323 o The unit of time in the skyline plot and in the new plots can
1324 now be chosen to be actual years, rather than substitutions.
1328 CHANGES IN APE VERSION 1.2-3
1333 o The new function rtree() generates a random binary tree with or
1334 without branch lengths.
1336 o Two new functions for drawing lineages-through-time (LTT) plots
1337 are provided: ltt.lines() adds a LTT curve to an existing plot,
1338 and mltt.plot() does a multiple LTT plot giving several trees as
1339 arguments (see `?ltt.plot' for details).
1344 o Some taxon names made R crashing when calling as.phylo.hclust():
1347 o dist.dna() returned an error with two identical DNA sequences
1348 (only using the Jukes-Cantor method returned 0): this is fixed.
1353 o The function dist.phylo() has been re-written using a different
1354 algorithm: it is now about four times faster.
1356 o The code of branching.times() has been improved: it is now about
1361 CHANGES IN APE VERSION 1.2-2
1366 o The new function seg.sites() finds the segregating sites in a
1367 sample of DNA sequences.
1372 o A bug introduced in read.tree() and in read.nexus() with version
1375 o A few errors were corrected and a few examples were added in the
1380 CHANGES IN APE VERSION 1.2-1
1385 o plot.phylo() can now draw the edge of the root of a tree if it
1386 has one (see the new option `root.edge', its default is FALSE).
1391 o A bug was fixed in read.nexus(): files with semicolons inside
1392 comment blocks were not read correctly.
1394 o The behaviour of read.tree() and read.nexus() was corrected so
1395 that tree files with badly represented root edges (e.g., with
1396 an extra pair of parentheses, see the help pages for details)
1397 are now correctly represented in the object of class "phylo";
1398 a warning message is now issued.
1402 CHANGES IN APE VERSION 1.2
1407 o plot.phylo() has been completely re-written and offers several
1408 new functionalities. Three types of trees can now be drawn:
1409 phylogram (as previously), cladogram, and unrooted tree; in
1410 all three types the branch lengths can be drawn using the edge
1411 lengths of the phylogeny or not (e.g., if the latter is absent).
1412 The vertical position of the nodes can be adjusted with two
1413 choices (see option `node.pos'). The code has been re-structured,
1414 and two new functions (potentially useful for developpers) are
1415 documented separately: node.depth.edgelength() and node.depth();
1416 see the respective help pages for details.
1418 o The new function zoom() allows to explore very large trees by
1419 focusing on a small portion of it.
1421 o The new function yule() fits by maximum likelihood the Yule model
1422 (birth-only process) to a phylogenetic tree.
1424 o Support for writing DNA sequences in FASTA format has been
1425 introduced in write.dna() (support for reading sequences in
1426 this format was introduced in read.dna() in version 1.1-2).
1427 The function has been completely re-written, fixing some bugs
1428 (see below); the default behaviour is no more to display the
1429 sequences on the standard output. Several options have been
1430 introduced to control the sequence printing in a flexible
1431 way. The help page has been extended.
1433 o A new data set is included: a supertree of bats in NEXUS format.
1438 o In theta.s(), the default of the option `variance' has
1439 been changed to `FALSE' (as was indicated in the help page).
1441 o Several bugs were fixed in the code of all.equal.phylo().
1443 o Several bugs were fixed in write.dna(), particularly this
1444 function did not work with `format = "interleaved"'.
1446 o Various errors were corrected in the help pages.
1451 o The argument names of as.hclust.phylo() have been changed
1452 from "(phy)" to "(x, ...)" to conform to the definition of
1453 the corresponding generic function.
1455 o gamma.stat() has been renamed gammaStat() to avoid confusion
1456 since gamma() is a generic function.
1460 CHANGES IN APE VERSION 1.1-3
1465 o base.freq() previously did not return a value of 0 for
1466 bases absent in the data (e.g., a vector of length 3 was
1467 returned if one base was absent). This is now fixed (a
1468 vector of length 4 is always returned).
1470 o Several bugs were fixed in read.nexus(), including that this
1471 function did not work in this absence of a "TRANSLATE"
1472 command in the NEXUS file, and that the commands were
1477 CHANGES IN APE VERSION 1.1-2
1482 o The Tamura and Nei (1993) model of DNA distance is now implemented
1483 in dist.dna(): five models are now available in this function.
1485 o A new data set is included: a set of 15 sequences of the
1486 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1492 o A bug in read.nexus() was fixed.
1494 o read.dna() previously did not work correctly in most cases.
1495 The function has been completely re-written and its help page
1496 has been considerably extended (see ?read.dna for details).
1497 Underscores (_) in taxon names are no more replaced with
1498 spaces (this behaviour was undocumented).
1500 o A bug was fixed in write.dna().
1504 CHANGES IN APE VERSION 1.1-1
1509 o A bug in read.tree() introduced in APE 1.1 was fixed.
1511 o A bug in compar.gee() resulted in an error when trying to fit
1512 a model with `family = "binomial"'. This is now fixed.
1516 CHANGES IN APE VERSION 1.1
1521 o The Klastorin (1982) method as suggested by Misawa and Tajima
1522 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1523 on the basis of phylogenetic trees has been implemented (see
1524 the function klastorin()).
1526 o Functions have been added to convert APE's "phylo" objects in
1527 "hclust" cluster objects and vice versa (see the help page of
1528 as.phylo for details).
1530 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1531 are introduced for the estimation of absolute evolutionary rates
1532 (ratogram) and dated clock-like trees (chronogram) from
1533 phylogenetic trees using the non-parametric rate smoothing approach
1534 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1536 o A summary method is now provided printing a summary information on a
1537 phylogenetic tree with, for instance, `summary(tree)'.
1539 o The behaviour of read.tree() was changed so that all spaces and
1540 tabulations in tree files are now ignored. Consequently, spaces in tip
1541 labels are no more allowed. Another side effect is that read.nexus()
1542 now does not replace the underscores (_) in tip labels with spaces
1543 (this behaviour was undocumented).
1545 o The function plot.phylo() has a new option (`underscore') which
1546 specifies whether the underscores in tip labels should be written on
1547 the plot as such or replaced with spaces (the default).
1549 o The function birthdeath() now computes 95% confidence intervals of
1550 the estimated parameters using profile likelihood.
1552 o Three new data sets are included: a gene tree estimated from 36
1553 landplant rbcL sequences, a gene tree estimated from 32 opsin
1554 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1559 o A bug was fixed in dist.gene() where nothing was returned.
1561 o A bug in plot.mst() was fixed.
1563 o A bug in vcv.phylo() resulted in false correlations when the
1564 option `cor = TRUE' was used (now fixed).
1568 CHANGES IN APE VERSION 1.0
1573 o Two new functions, read.dna() and write.dna(), read/write in a file
1574 DNA sequences in interleaved or in sequential format.
1576 o Two new functions, read.nexus() and write.nexus(), read/write trees
1579 o The new function bind.tree() allows to bind two trees together,
1580 possibly handling root edges to give internal branches.
1582 o The new function drop.tip() removes the tips in a phylogenetic tree,
1583 and trims (or not) the corresponding internal branches.
1585 o The new function is.ultrametric() tests if a tree is ultrametric.
1587 o The function plot.phylo() has more functionalities such as drawing the
1588 branches with different colours and/or different widths, showing the
1589 node labels, controling the position and font of the labels, rotating
1590 the labels, and controling the space around the plot.
1592 o The function read.tree() can now read trees with no branch length,
1593 such as "(a,b),c);". Consequently, the element `edge.length' in
1594 objects of class "phylo" is now optional.
1596 o The function write.tree() has a new default behaviour: if the default
1597 for the option `file' is used (i.e. file = ""), then a variable of
1598 mode character containing the tree in Newick format is returned which
1599 can thus be assigned (e.g., tree <- write.tree(phy)).
1601 o The function read.tree() has a new argument `text' which allows
1602 to read the tree in a variable of mode character.
1604 o A new data set is included: the phylogenetic relationships among
1605 the orders of birds from Sibley and Ahlquist (1990).
1609 CHANGES IN APE VERSION 0.2-1
1614 o Several bugs were fixed in the help pages.
1618 CHANGES IN APE VERSION 0.2
1623 o The function write.tree() writes phylogenetic trees (objects of class
1624 "phylo") in an ASCII file using the Newick parenthetic format.
1626 o The function birthdeath() fits a birth-death model to branching times
1627 by maximum likelihood, and estimates the corresponding speciation and
1630 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1633 o The function is.binary.tree() tests whether a phylogeny is binary.
1635 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1636 as well as some methods are introduced.
1638 o Several functions, including some generics and methods, for computing
1639 skyline plot estimates (classic and generalized) of effective
1640 population size through time are introduced and replace the function
1641 skyline.plot() in version 0.1.
1643 o Two data sets are now included: the phylogenetic relationships among
1644 the families of birds from Sibley and Ahlquist (1990), and an
1645 estimated clock-like phylogeny of HIV sequences sampled in the
1646 Democratic Republic of Congo.
1649 DEPRECATED & DEFUNCT
1651 o The function skyline.plot() in ape 0.1 has been deprecated and
1652 replaced by more elaborate functions (see above).
1657 o Two important bugs were fixed in plot.phylo(): phylogenies with
1658 multichotomies not at the root or not with only terminal branches,
1659 and phylogenies with a single node (i.e. only terminal branches)
1660 did not plot. These trees should be plotted correctly now.
1662 o Several bugs were fixed in diversi.time() in the computation of
1665 o Various errors were corrected in the help pages.