NEWS

---

phangorn 2.12.1.1

OTHER CHANGES

• improvements to write.ancestral
• bab got a progress bar, as it might runs for a long time (suggestion by Bárbara Bitarello).

phangorn 2.12.0

NEW FEATURES

• new function supgma, performing serial sampled UPGMA (Drummond, Rodrigo 2000)
• new function gap_as_state, treating gaps as a state.
• new function keep_as_tip allows to prune a tree and keep nodes as a tip (suggested by Hedvig Skirgård)
• nnls now can estimate trees with calibrations and tip dated trees
• the functions Descendants, Ancestors, Siblings, mrca.phy now also accept a character vector for the node argument and not only integers.
• Ancestral state reconstruction was rewritten. The output of ancestral.pars and ancestral.pars could return different objects. anc_pml and anc_pars are now prefered over ancestral.pml and ańcestral.pars. Output is now an object of class ancestral, which contains tree with node labels, the original alignment and reconstructions. The should be considered experimental as the internals of this function might change in future. Ancestral states of constant sites are now always this state.
• Joint reconstruction for ML is now available.
• Improvements to several plot functions to get nicer plots out of the box. Nicer defaults for plot.pml, mainly for rooted trees.
• plotAnc got an argument scheme allowing to use different color schemes, especially for amino acid models shared with image.AAbin and assumes an ancestral object.
• plot.networx gets two additional arguments, direction as in plot.phylo and angle to rotate the network.
• new function composition_test, indicating possible problems with base / state composition, similar to the test in iqtree.

OTHER CHANGES

• pml.control got an argument statefreq, which controls if "empirical" or (ML) "estimated" state/base frequencies are used/computed. The change of the default to "empirical" speeds up functions modelTest and pml_bb/optim.pml. However estimates will differ to previous versions, which were implicitly using "estimated".
• some improvements to pmlPart.
• the sankoff algorithm has been rewritten.

BUG FIXES

• pml_bb roots the tree, if method is either ultrametric or tipdated. Fixes problem when modelTest object was supplied.
• nnls.tree now checks if the tree has singletons.

phangorn 2.11.0

OTHER CHANGES

• Vignettes have been reorganised, rewritten and vastly improved thanks to Iris.
• small improvements to plot.codonTest, plot.networx
• rell bootstrap values are now computed by default in optim.pml / pml_bb

BUG FIXES

• fixed bug which caused warning on CRAN
• densiTree does not draw an empty plot any more
• Replace rgl.texts with texts3d, pull request by Duncan Murdoch (thanks)
• changes in read.nexus.splits and read.nexus.networx to work with the moving targets SplitsTree6/SplitsTreeCE

phangorn 2.10.0 (2022-09-18)

NEW FEATURES

• several improvements to simplify workflow and flatten learning curve.
• new function pml_bb, combining generation of starting trees, pml and optim.pml and allowing modelTest object as input.
• tipdated phylogenies estimation (was with limitations possible before, but not documented).
• Mkv model, edge length and rearrangements only work for ultrametric and tiplabeled phylogenies so far.
• Added experimental version of RELL bootstrap (Minh et al. 2013 Ultrafast Approximation for Phylogenetic Bootstrap).
• modelTest now tests several models for USER defined data.

OTHER CHANGES

• some default values of of pratchet changed
• updated, improved and reorganized several vignettes.
• function allSitePattern got an argument additional type.

phangorn 2.9.0 (2022-06-16)

BUG FIXES

• modelTest did not work if no tree was supplied

NEW FEATURES

• some tidy functions: glance.phyDat, tidy.modelTest

OTHER CHANGES

• dist.ml is a lot faster for the JC69 and F81 models if there are no ambiguous sites present.
• added a few helper function to simplifiy some workflows (e.g. modelTest)

phangorn 2.8.0 (2021-11-09)

BUG FIXES

• Use USE_FC_LEN_T in the C prototypes of LAPACK functions to correspond to code produced by gfortran >= 7. The mechanism was introduced in R 3.6.2 and is planned to make its use obligatory in R 4.2.0.
• bug in dna2codon fixed.
• codon models (codonTest) most likely did not work properly for models other than the standard code.

NEW FEATURES

• free rate model
• Mkv model (so far only for rooted trees)
• better support for ultrametric and time trees

OTHER CHANGES

• optim.pml has internally been reorganized to be easier to maintain and extend.
• pml.control got an additional argument tau which controls the minimal edge length during optimisation.
• trees constructed with allCompat, maxCladeCred now have support values stored in the node.labels
• switched from magrittr %>% to the native pipe |> dropped dependency on magrittr

phangorn 2.7.1 (2021-07-13)

BUG FIXES

• several bug fixes in parsimony code

phangorn 2.7.0 (2021-05-03)

BUG FIXES

• several bug fixes, e.g. which called bootstrap.pml and pratchet to crash

OTHER CHANGES

• internal functions for handling bipartitions have been harmonized with ape and some functions like maxCladeCred are faster

phangorn 2.6.0

NEW FEATURES

• transfer bootstrap (Lemoine et al. 2018)
• pratchet saves trees visited during search, which can be used as (approximate) bootstrap values
• rewritten fitch algorithm to be more memory efficient, often faster and without limitation on the number of states
• dist.hamming may handle larger datasets and can be faster
• add Laguerre quadrature as option for discrete rate classes (experimental)
• additional genetic codes for codon models.

OTHER CHANGES

• conversion between alignment formats is faster and more memory efficient, allowing the handling of larger datasets
• changed R dependencies to 3.6.0 mainly to supply nicer palettes via hcl.colors()
• lots of small improvements to especially for codon models
• tests are now done by tinytest, dropped dependencies on testthat, vdiffr
• all vignettes are now based on Rmarkdown
• pmlPart and pmlMix are a bit more robust

phangorn 2.5.4

NEW FEATURES

• dist.ml, dist.hamming, dist.logDet and dist.p also take DNAbin or AAbin objects as input

BUG FIXES

• bootstrap.pml returned an error with argument optNni=T Best practise is to always use TRUE and not T as shortcut

OTHER CHANGES

• several more unit tests

phangorn 2.5.2

NEW FEATURES

• pratchet, optim.parsimony, optim.pml all may now return trees with multifurcations in case duplicated sequences are discovered. This may lead to speeding up computations and improved tree topology search.
• function codonTest which adds codon models to detect positive selection (M1a, M2a) and several options to estimate codon frequencies (F3x4, F1x4). Can be pretty slow and still experimental.
• broom type tidy function for several objects to easier compare models
• new "equal_angle" layout for 2D-networks (now the default), gives usually nicer layout of phylogenetic networks
• tiplabels, nodelabels, edgelabels from ape work for plot.networx if plotted with base R

OTHER CHANGES

• several small improvements to more intuitively use pml and phyDat objects, like subsetting phyDat objects with "[i, j]".
• several more unit tests
• two new contributors, Keren and Richel
• optim.parsimony, pratchet, pmlMix and pmlPart may return the current best tree or object when interrupted.
• roxygen2 is used to generate NAMESPACE file

phangorn 2.4.0 (2018-02-15)

NEW FEATURES

• new function add.tips

BUG FIXES

• midpoint works now for trees with only 2 tips
• densiTree, bug report by Richel Bilderbeek
• tree rearrangement in optim.pml return tree with double edge matrix
• phyDat should work now for named vectors

OTHER CHANGES

• many more unit tests
• more consistent coding style
• flashClust and seqLogo are not suggested packages any more

phangorn 2.3.0

NEW FEATURES

• new function mast to compute the maximum agreement subtree
• identify.networx to identify splits in a network
• densiTree got more attributes
• unique.dist, to filter duplicate distances
• ancestral.pml and ancestral.pars are now may return proper phyDat objects and in for DNA may return ambiguous states

BUG FIXES

• densiTree may if the consensus tree had different ordering of labels

OTHER CHANGES

• acctran allows multiPhylo objects as input
• rNNI has been completely rewritten and is faster

phangorn 2.2.0 (2017-04-03)

NEW FEATURES

• midpoint in now generic and works for multiPhylo objects
• as.bitsplits.splits to better interact with ape

BUG FIXES

• bug fix in RI and CI for ambiguous data

OTHER CHANGES

• added roxygen2 documentation, so R code is now much better documented, reorganisation of some documentation
• many more unit tests

phangorn 2.1.0

NEW FEATURES

• new functions to compute the (approximate) SPR distance (sprdist, SPR.dist) contributed by Leonardo de Oliveira Martins.
• super tree methods based on NNI and SPR distances

BUG FIXES

• fixed bug in KF.dist

OTHER CHANGES

• improvements to as.networx. It often now produces networks with less edges resulting in much nicer plots
• plot.networx does take a different layout algorithm
• as.data.frame.phyDat and as.character.phyDat return amino acids now in upper cases
• more unit tests
• improved cbind.phyDat, faster and more flexible
• phangorn now requires ape 4.0
• phangorn now imports Rcpp, but not nnls any more

phangorn 2.0.4 (2016-06-21)

NEW FEATURES

• new weighted Robinson-Foulds (1979) distance wRF, suggested by Michelle Kendall and normalized Robinson-Foulds suggested by Sereina Rutschmann
• codon model "YN98" can be called directly, improved documentation
• bootstrap.phyDat got an new argument jumble, which randomizes input order of sequences

OTHER CHANGES

• more unit tests

phangorn 2.0.3 (2016-05-01)

NEW FEATURES

• new function maxCladeCred computing the maximum clade credibility tree from a sample of trees
• function read.nexus.networx and write.nexus.networx to import / export phylogenetic networx to SplitsTree
• function as.AAbin.phyDat to exchange data with the new AAbin class from ape
• likelihood ratchet (Vos 2003) topology optimisation in optim.pml
• with KF.dist (Kuhner & Felsenstein) and path.dist can be used like RF.dist

BUG FIXES

• improvements to optim.pml to avoid numerical problems, can now handle much more taxa (still experimantal)

OTHER CHANGES

• mrca.phylo can be used like mrca from ape (faster for large trees)
• individual splits can be colored in lento plots (suggested by France Thouzé)
• plot.networx now (silently) returns a networx object with some of the graphics parameters, more plot options
• lots of small changes to make handling and identifying splits, edges in trees and networks easier
• plotBS has a new argument frame and arguments BStrees can be empty
• new vignette IntertwiningTreesAndNetworks

phangorn 2.0.2 (2016-01-23)

OTHER CHANGES

• phangorn now suggests only the Biostrings and not depends on it
• some improvements to bab (branch and bound), may be faster

phangorn 2.0.0 (2015-12-10)

NEW FEATURES

• as.phyDat.MultipleAlignment to excange data with Biostrings
• dist.ml can now compute distances using a discrete gamma model and the "F81" model.
• optim.pml got a new rearrangement argument and can now use a stochastic rearrangements similar to Nguyen et al. (2015)

BUG FIXES

• plotBS may double counted edges when rooted trees were in the sample

OTHER CHANGES

• optim.pml uses more C code and should be more robust
• more unit tests
• baseFreq got additional parameter 'all' similar to base.freq in ape
• lots of little improvements in the manual and help files
• modelTest now also shows AIC weights and model="all" will test all available models

phangorn 1.99.14 (2015-07-09)

NEW FEATURES

• phyDat2alignment to exports files to seqinr
• readDist, writeDist to import / export distance matrices
• cophenetic distance function for splits and networx
• added unit tests

BUG FIXES

• as.splits.networx did not work properly for 4 taxa (reported by Laurélène Faye)
• RF.dist returned sometimes wrong values (reported by Andres Dajles)
• plotBS did sometimes not work if the tree had no edge lengths
• plotBS did not work propoerly if input trees were rooted (reported by Quynh Quach)
• plot.networx ignored cex argument in "2D" plots
• Siblings ignored include.self argument if node is a vector

OTHER CHANGES

• plotBS got an additional argument p to plot only support values greater than p
• pml and optim.pml now uses more C-code (and is a bit faster)
• defaults in modelTest changed
• discrete.gamma is now exported in the NAMESPACE

phangorn 1.99-13 (2015-04-08)

OTHER CHANGES

• improved importing and conversion of data
• improved stability of pml and optim.pml

phangorn 1.99-12 (2015-02-14)

NEW FEATURES

• added neighborNet algorithm (Bryant and Moulton 2004) very experimental at the moment

BUG FIXES

• plotBS was not working correctly if bootstraped trees are in compressed form (bug report by Tobias Müller)

OTHER CHANGES

• many splits and networx methods have been improved and a vignette was added
• phangorn now suggests only the rgl and not depends on it to avoid problems on different platforms (suggestion by Matt Pennell)
• new package dependencies knitr for html vignettes and nnls

phangorn 1.99-10

BUG FIXES

• reorder.networx may not work as expected
• Gamma model was not working properly in simSeq.pml

phangorn 1.99-9 (2014-10-09)

BUG FIXES

• bug fixes for clang environment
• midpoint takes care of node labels

phangorn 1.99-8 (2014-10-06)

NEW FEATURES

• pmlPart got an argument rooted to handle rooted trees
• simSeq is now a generic function. This simplifies the construcion of parametric bootstrap test
• SOWH.test (very experimental)
• as.networx and plot.networx improved considerably (often generate networks less edges) and planar graphs are now plotted nicely

BUG FIXES

• fixed some bugs in ancestral.pars
• amino acid model "Blosum62" was not working

OTHER CHANGES

• improvements to read.nexus.splits, write.nexus.splits to be more consistant with SplitsTree
• splitsNetwork got an additional argument splits
• help for consensusNet, as.splits, as.networx have been reorganised and improved
• treedist is much faster for larger trees
• several changes to keep R CMD check happy
• a development version phangorn is now available on github https://github.com/KlausVigo/phangorn.git

phangorn 1.99-6

NEW FEATURES

• cladePar helps coloring trees
• treedist is faster for larger trees, better documentation and examples

BUG FIXES

• the plot of consensusNet shows now the proper bootstrap values

OTHER CHANGES

• phangorn does not depend only suggest rgl (should build on OS X now)
• default rearrangement for parsimony is now "SPR"

phangorn 1.99-5 (2014-01-02)

NEW FEATURES

• RF.dist works also on "multiPhylo" objects and is quite fast
• optim.pml can now handle NNI tree arrangements for rooted trees, still experimental but useful for dating etc.

BUG FIXES

• rNNI did return sometimes trees without tip labels
• SH.test did not work for pmlCluster objects
• df for rooted rooted/ultrametric trees are correctly computed

OTHER CHANGES

• lots of internal code C-code changed
• exports of some of the internal ML function, this should speed up in future other packages e.g. the colescentMCMC package, which use them considerably (interface may changes in the future)
• registered C routines

phangorn 1.99-0

NEW FEATURES

• new function dist.p to estimate pairwise polymorphism p-distances from DNA sequences

BUG FIXES

• as.data.frame.phyDat returned only site patterns and so did write.phyDat for nexus files
• some of the recently introduced (1.7-4) amino acid models were not known by all functions and contained NAs

OTHER CHANGES

• changed package imports and depends structure to aviod error messages, thanks to Brian Ripley
• a lot of the internal C-code has changed

phangorn 1.7-4 (2013-04-04)

NEW FEATURES

• densiTree plots are available now
• new species tree and super tree methods
• more amino acid models

BUG FIXES

• phangorn now depends on rgl instead of suggests rgl, rgl wants to be loaded before igraph, otherwise a compiling error on some platforms occured!
• fixed a bug that sometimes caused in pratched to crash
• fixed a bug when using negative indices in subset.phyDat
• the search heuristic SPR in optim.parsimony evaluates now more trees and is more likely to find better ones

OTHER CHANGES

• underlying C-code for several functions has changed. less memory reallocations and potentially time savings hopefully I included not too many bugs
• optimising edge length changed from Jacobi to Gauss-Seidel method and will hopefully be more robust in the long term!
• Descendants is much faster for option type="all"
• plotAnc gives user more control and produces nicer plots

phangorn 1.7-1 (2012-10-30)

NEW FEATURES

• pmlPart got additional argument model (request from Santiago Claramunt)

BUG FIXES

• pmlPart should be more robust

OTHER CHANGES

• started reorganising the code
• underlying code of several parsimony functions has changed and these are now considerably faster
• some examples are changed to allow faster checking on CRAN

phangorn 1.6-5 (2012-10-10)

NEW FEATURES

• dist.hamming handles ambigious states now as dist.ml (request from Arne Mooers)

BUG FIXES

• phangorn links properly to ape

phangorn 1.6-3 (2012-07-01)

NEW FEATURES

• optim.parsimony has a new search heuristic (SPR)

BUG FIXES

• changed package to work with igraph >= 0.6

OTHER CHANGES

• arguments of pratchet changed

phangorn 1.6-0 (2012-04-05)

NEW FEATURES

• dist.ml has more options and is faster (ca. 5 times for nucleotides and 20 times for amino acids)

BUG FIXES

• plotBS did not work properly with ape version 3.0

OTHER CHANGES

• vignettes changed for a faster compilation of the package
• Ancestors allows a vector of nodes as input
• midpoint uses less memory and works for larger trees (10000 of tips)
• ancestral.pars gives better formated output

phangorn 1.5-1 (2011-12-13)

OTHER CHANGES

• several examples changed for a faster compilation of the package

phangorn 1.5-0 (2011-12-10)

NEW FEATURES

• codon models can be used directly (dn/ds ratio can be computed)
• modelTest works now also for amino acids

BUG FIXES

• the code to compute RI and CI changed and should be more robust

OTHER CHANGES

• package parallel is used instead of multicore
• vignettes, examples, help improved
• ChangeLog is called NEWS

phangorn 1.4-1 (2011-06-30)

NEW FEATURES

• parsimony branch-and-bould algorithms bab (so far pretty slow and memory intensive)
• more amino acid models
• function nnls.tree to compute non-negative edge weights for a given tree and a distance matrix

BUG FIXES

• allTrees returns now an integer edge matrix, this could have caused some problems previously
• CI and RI now take better care of ambiguous states
• dist.ml has default value for amino acids
• as.splits.multiPhylo produces more sensible bipartitions and so lento and consensusNet produce more useful plots (thanks to Emmanuel Paradis)

OTHER CHANGES

• several changes to the networx classes and methods
• modelTest now also returns the function calls of the estimated models, which can be used in downstream analyses
• vignette "Trees" has a few more examples
• dist.ml is more general (base frequencies and rate matrix can be supplied)
• pml objects are more compact, thanks to the Matrix package
• xtable is now a suggested package (needed for vignettes)

phangorn 1.4-0 (2011-03-27)

NEW FEATURES

• plot.network to plot split networks in 3D (requires rgl) and 2D (still very experimantal)
• consensusNet computes consensus networks
• Lento plot allows to take multiPhylo objects as input

BUG FIXES

• CI and RI did not work with only one site pattern present
• pratchet returned only one, not all of the best trees found

OTHER CHANGES

• phangorn now requires the Matrix, igraph and rgl packages
• designTree returns a sparse Matrix and this can save a lot of memory
• internal code for computing bipartitions is much faster for large trees, and so are several functions depending on it, e.g. RF.dist, treedist, Descendants

phangorn 1.3-1 (2011-02-14)

BUG FIXES

• the multicore package may failed, if executed in a GUI environment, more error checks included
• optim.pml, in rare cases may failed to optimize edge length (should be more robust now)

OTHER CHANGES

• some changes to keep R CMD check happy
• modelTest, pratchet, bootstrap.pml, bootstrap.phyDat got an additional argument multicore option to switch between serial and parallel execution

phangorn 1.3-0 (2011-01-31)

NEW FEATURES

• acctran to assign edge length to parsimony trees

OTHER CHANGES

• phangorn can now be cited
• additional and improved ancestral reconstructions methods (ACCTRAN, MPR)
• new vignette describing ancestral sequence reconstruction

phangorn 1.2-0 (2010-11-22)

NEW FEATURES

• new function pratchet (parsimony ratchet)
• new function midpoint for rooting trees
• new function pruneTree to build concensus trees from node labels (e.g. bootstrap values)
• multicore support for modelTest

BUG FIXES

• ancestral.pars sometimes did not show all possible states
• the call-attributes did not get proper changed in update.pml and optim.pml

OTHER CHANGES

• there is now a general help page displayed with '?phangorn'
• dist.hamming is faster
• getClans, getSlices and getDiverstity can now handle multifurcating trees

phangorn 1.1-2 (2010-09-21)

NEW FEATURES

• more generic methods for class splits (print, as.matrix)
• plotBS can plot now cladograms and phylograms

BUG FIXES

• read.phyDat sometimes did not work properly for amino acids

phangorn 1.1-1 (2010-09-03)

NEW FEATURES

• optim.pml allows to optimize rooted trees

OTHER CHANGES

• description of getClans improved

phangorn 1.1-0 (2010-08-28)

NEW FEATURES

• Consistency Index (CI) and and Rentention Index (RI)
• clanistic tools
• new generic function cbind.phyDat
• optim.parsimony works now also with the fitch algorithm, faster than the sankoff version

BUG FIXES

• treedist and RF.dist now check whether trees are binary and try to handle multifurcations (thanks to Jeremy Beaulieu for bug fixes)

OTHER CHANGES

• second vignette describing some special features
• allTrees is faster
• trace and pml.control are now more consistent
• optim.pml uses less memory and can be faster for data with lots of characters

phangorn 1.0-2 (2010-05-16)

BUG FIXES

• pml.control did not work properly

OTHER CHANGES

• pmlCluster, pmlMix and pmlPart gained an attribute control, which controls the outermost loop
• some more error checking for pml and parsimony classes (thanks to Emmanuel and Liat)

phangorn 1.0-1 (2010-04-15)

NEW FEATURES

• ancestral sequence reconstruction (parsimony and likelihood based)
• a small convenience function acgt2ry for ry-coding
• as.phylo.splits computes a tree from compatible splits

BUG FIXES

• a small error in pmlCluster was fixed

OTHER CHANGES

• upgma changed to accommodate change in as.phylo.hclust
• lento plots are looking nicer

phangorn 1.0-0 (2010-03-18)

NEW FEATURES

• implementation of many nucleotide substitution models (additional general transition models can be defined)
• new function modelTest, comparison of different phylogenetic model with AIC or BIC
• Lento plot
• subset functions for phyDat objects

BUG FIXES

• an error in pace is fixed

OTHER CHANGES

• parsimony (fitch and sankoff) can now handle multiPhylo objects
• splits structure (which is a list of bipartitions), used by lento and hadamard conjugation
• phyDat objects can be more general generated using a contrast matrix

phangorn 0.99-6 (2010-01-27)

NEW FEATURES

• pace, extracts the ancestral states of the root of a tree using the sankoff algorithm

BUG FIXES

• fixed a bug in dist.ml (thanks to Emmanuel)
• fixed a bug introduced to SH.test in 0.99-5

OTHER CHANGES

• fixed several spelling mistakes in the documentation

phangorn 0.99-5 (2010-01-15)

NEW FEATURES

• parallel computing via multicore (so far bootstrap.pml, bootstrap.pml profit under linux)
• compute edge weights for parsimony trees

BUG FIXES

• optim.pml had problems when
• as.character converted ?,- wrongly to NA
• fitch needed binary trees as input, otherwise pscore is likely to be wrong (returns now a warning)
• optim.pml had a problem with identical sequences

OTHER CHANGES

• optim.parsimony returns now a tree with edge weights
• vignette is enhanced, I fixed some spelling mistakes and added some more examples.

phangorn 0.99-4 (2009-11-27)

NEW FEATURES

• new generic function unique.phyDat

OTHER CHANGES

• internal data format phyDat changed and data are stored more memory efficient (optim.pml and friends use less memory and may be faster)

phangorn 0.99-3 (2009-10-30)

BUG FIXES

• RF.dist sometimes returned wrong distances
• rate parameter is now properly normalized in pml.Part and pmlCluster
• simSeq had problems simulating a single character

NEW FEATURES

• rSPR and rNNI to simulate tree rearrangements

phangorn 0.99-2 (2009-07-21)

NEW FEATURES

• bootstrap.pml and bootstrap.phyDat: parametric bootstrap methods
• simSeq: A new function to simulate sequence data
• read.phyDat: simplifies reading in alignments
• SH.test: Shimodaira-Hasegawa test
• RF.dist: Robinson-Foulds distance as replacement for treedist (uses less memory and is much faster)

BUG FIXES

• dist.ml returned wrong variances.
• as.character.phyDat, as.data.frame caused an error for alignments with only one site.

OTHER CHANGES

• added vignette describing how to perform some standard phylogenetic analysis with phangorn.
• more functions to convert between different data formats.
• NNI tree search is now general possible for partition models (pmlPart, pmlCluster)

phangorn 0.0-5 (2009-01-22)

BUG FIXES

• Solved a namespace problem with ape (>=2.2-3).

phangorn 0.0-4 (2008-12-22)

NEW FEATURES

• splitsNetwork fits a phylogenetic network using a L1 penalty. (High memory consumption)
• pmlPen: A new function to estimate penalized likelihood models for sets of edge weights in mixtures or partition models.

BUG FIXES

• dist.ml should be more forgiving for different inputs.

OTHER CHANGES

• a new dataset.

phangorn 0.0-3 (2008-10-29)

NEW FEATURES

• amino acid models
• several new maximum likelihood models: mixture models (pmlMix), and some model for phylogenomic data partition models (pmlPart), and clustering of partitions / genes (pmlCluster) (still experimental, feed back wellcome)
• design matrices for phylogenetic distance methods
• added some functions useful for simulations (nni, allTrees)

OTHER CHANGES

• the data object phyDat changed slightly internally
• a new dataset
• read.aa to read amino acid data in phylip format based on read.dna from the ape package

phangorn 0.0-2 (2008-07-21)

NEW FEATURES

• more generic functions (plot.pml, update.pml)

BUG FIXES

• the "Fitch" algorithm in parsimony contained a bug

OTHER CHANGES

• pml has a cleaner interface (less parameter)
• new faster parsimony analysis (more compiled C-Code)
• added NAMESPACE