NEWS

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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, oull reqiest 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