CHANGES in PHANGORN VERSION 2.11.0 OTHER CHANGES o Vignettes have been reorganised, rewritten and vastly improved thanks to Iris. o small improvements to plot.codonTest, plot.networx o rell bootstrap values are now computed by default in optim.pml / pml_bb BUG FIXES o fixed bug which caused warning on CRAN o densiTree does not draw an empty plot any more o Replace rgl.texts with texts3d, oull reqiest by Duncan Murdoch (thanks) o changes in read.nexus.splits and read.nexus.networx to work with the moving targets SplitsTree6/SplitsTreeCE CHANGES in PHANGORN VERSION 2.10.0 NEW FEATURES o several improvements to simplify workflow and flatten learning curve. o new function pml_bb, combining generation of starting trees, pml and optim.pml and allowing modelTest object as input. o tipdated phylogenies estimation (was with limitations possible before, but not documented). o Mkv model, edge length and rearrangements only work for ultrametric and tiplabeled phylogenies so far. o Added experimental version of RELL bootstrap (Minh et al. 2013 Ultrafast Approximation for Phylogenetic Bootstrap). o modelTest now tests several models for USER defined data. OTHER CHANGES o some default values of of pratchet changed o updated, improved and reorganized several vignettes. o function allSitePattern got an argument additional type. CHANGES in PHANGORN VERSION 2.9.0 BUG FIXES o modelTest did not work if no tree was supplied NEW FEATURES o some tidy functions: glance.phyDat, tidy.modelTest OTHER CHANGES o dist.ml is a lot faster for the JC69 and F81 models if there are no ambiguous sites present. o added a few helper function to simplifiy some workflows (e.g. modelTest) CHANGES in PHANGORN VERSION 2.8.0 BUG FIXES o 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. o bug in dna2codon fixed. o codon models (codonTest) most likely did not work properly for models other than the standard code. NEW FEATURES o free rate model o Mkv model (so far only for rooted trees) o better support for ultrametric and time trees OTHER CHANGES o optim.pml has internally been reorganized to be easier to maintain and extend. o pml.control got an additional argument tau which controls the minimal edge length during optimisation. o trees constructed with allCompat, maxCladeCred now have support values stored in the node.labels o switched from magrittr %>% to the native pipe |> dropped dependency on magrittr CHANGES in PHANGORN VERSION 2.7.1 BUG FIXES o several bug fixes in parsimony code CHANGES in PHANGORN VERSION 2.7.0 BUG FIXES o several bug fixes, e.g. which called bootstrap.pml and pratchet to crash OTHER CHANGES o internal functions for handling bipartitions have been harmonized with ape and some functions like maxCladeCred are faster CHANGES in PHANGORN VERSION 2.6.0 NEW FEATURES o transfer bootstrap (Lemoine et al. 2018) o pratchet saves trees visited during search, which can be used as (approximate) bootstrap values CHANGES in PHANGORN VERSION 2.6.0 NEW FEATURES o rewritten fitch algorithm to be more memory efficient, often faster and without limitation on the number of states o dist.hamming may handle larger datasets and can be faster o add Laguerre quadrature as option for discrete rate classes (experimental) o additional genetic codes for codon models. OTHER CHANGES o conversion between alignment formats is faster and more memory efficient, allowing the handling of larger datasets o changed R dependencies to 3.6.0 mainly to supply nicer palettes via hcl.colors() o lots of small improvements to especially for codon models o tests are now done by tinytest, dropped dependencies on testthat, vdiffr o all vignettes are now based on Rmarkdown o pmlPart and pmlMix are a bit more robust CHANGES in PHANGORN VERSION 2.5.4 NEW FEATURES o dist.ml, dist.hamming, dist.logDet and dist.p also take DNAbin or AAbin objects as input BUG FIXES o bootstrap.pml returned an error with argument optNni=T Best practise is to always use TRUE and not T as shortcut OTHER CHANGES o several more unit tests CHANGES in PHANGORN VERSION 2.5.2 NEW FEATURES o 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. o 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. o broom type tidy function for several objects to easier compare models o new "equal_angle" layout for 2D-networks (now the default), gives usually nicer layout of phylogenetic networks o tiplabels, nodelabels, edgelabels from ape work for plot.networx if plotted with base R OTHER CHANGES o several small improvements to more intuitively use pml and phyDat objects, like subsetting phyDat objects with "[i, j]". o several more unit tests o two new contributors, Keren and Richel o optim.parsimony, pratchet, pmlMix and pmlPart may return the current best tree or object when interrupted. o roxygen2 is used to generate NAMESPACE file CHANGES in PHANGORN VERSION 2.4.0 NEW FEATURES o new function add.tips BUG FIXES o midpoint works now for trees with only 2 tips o densiTree, bug report by Richel Bilderbeek o tree rearrangement in optim.pml return tree with double edge matrix o phyDat should work now for named vectors OTHER CHANGES o many more unit tests o more consistent coding style o flashClust and seqLogo are not suggested packages any more CHANGES in PHANGORN VERSION 2.3.0 NEW FEATURES o new function mast to compute the maximum agreement subtree o identify.networx to identify splits in a network o densiTree got more attributes o unique.dist, to filter duplicate distances o ancestral.pml and ancestral.pars are now may return proper phyDat objects and in for DNA may return ambiguous states BUG FIXES o densiTree may if the consensus tree had different ordering of labels OTHER CHANGES o acctran allows multiPhylo objects as input o rNNI has been completely rewritten and is faster CHANGES in PHANGORN VERSION 2.2.0 NEW FEATURES o midpoint in now generic and works for multiPhylo objects o as.bitsplits.splits to better interact with ape BUG FIXES o bug fix in RI and CI for ambiguous data OTHER CHANGES o added roxygen2 documentation, so R code is now much better documented, reorganisation of some documentation o many more unit tests CHANGES in PHANGORN VERSION 2.1.0 NEW FEATURES o new functions to compute the (approximate) SPR distance (sprdist, SPR.dist) contributed by Leonardo de Oliveira Martins. o super tree methods based on NNI and SPR distances BUG FIXES o fixed bug in KF.dist OTHER CHANGES o improvements to as.networx. It often now produces networks with less edges resulting in much nicer plots o plot.networx does take a different layout algorithm o as.data.frame.phyDat and as.character.phyDat return amino acids now in upper cases o more unit tests o improved cbind.phyDat, faster and more flexible o phangorn now requires ape 4.0 o phangorn now imports Rcpp, but not nnls any more CHANGES in PHANGORN VERSION 2.0.4 NEW FEATURES o new weighted Robinson-Foulds (1979) distance wRF, suggested by Michelle Kendall and normalized Robinson-Foulds suggested by Sereina Rutschmann o codon model "YN98" can be called directly, improved documentation o bootstrap.phyDat got an new argument jumble, which randomizes input order of sequences OTHER CHANGES o more unit tests CHANGES in PHANGORN VERSION 2.0.3 NEW FEATURES o new function maxCladeCred computing the maximum clade credibility tree from a sample of trees o function read.nexus.networx and write.nexus.networx to import / export phylogenetic networx to SplitsTree o function as.AAbin.phyDat to exchange data with the new AAbin class from ape o likelihood ratchet (Vos 2003) topology optimisation in optim.pml o with KF.dist (Kuhner & Felsenstein) and path.dist can be used like RF.dist BUG FIXES o improvements to optim.pml to avoid numerical problems, can now handle much more taxa (still experimantal) OTHER CHANGES o mrca.phylo can be used like mrca from ape (faster for large trees) o individual splits can be colored in lento plots (suggested by France Thouzé) o plot.networx now (silently) returns a networx object with some of the graphics parameters, more plot options o lots of small changes to make handling and identifying splits, edges in trees and networks easier o plotBS has a new argument frame and arguments BStrees can be empty o new vignette IntertwiningTreesAndNetworks CHANGES in PHANGORN VERSION 2.0.2 OTHER CHANGES o phangorn now suggests only the Biostrings and not depends on it o some improvements to bab (branch and bound), may be faster CHANGES in PHANGORN VERSION 2.0.0 NEW FEATURES o as.phyDat.MultipleAlignment to excange data with Biostrings o dist.ml can now compute distances using a discrete gamma model and the "F81" model. o optim.pml got a new rearrangement argument and can now use a stochastic rearrangements similar to Nguyen et al. (2015) BUG FIXES o plotBS may double counted edges when rooted trees were in the sample OTHER CHANGES o optim.pml uses more C code and should be more robust o more unit tests o baseFreq got additional parameter 'all' similar to base.freq in ape o lots of little improvements in the manual and help files o modelTest now also shows AIC weights and model="all" will test all available models CHANGES in PHANGORN VERSION 1.99.14 NEW FEATURES o phyDat2alignment to exports files to seqinr o readDist, writeDist to import / export distance matrices o cophenetic distance function for splits and networx o added unit tests BUG FIXES o as.splits.networx did not work properly for 4 taxa (reported by Laurélène Faye) o RF.dist returned sometimes wrong values (reported by Andres Dajles) o plotBS did sometimes not work if the tree had no edge lengths o plotBS did not work propoerly if input trees were rooted (reported by Quynh Quach) o plot.networx ignored cex argument in "2D" plots o Siblings ignored include.self argument if node is a vector OTHER CHANGES o plotBS got an additional argument p to plot only support values greater than p o pml and optim.pml now uses more C-code (and is a bit faster) o defaults in modelTest changed o discrete.gamma is now exported in the NAMESPACE CHANGES in PHANGORN VERSION 1.99-13 OTHER CHANGES o improved importing and conversion of data o improved stability of pml and optim.pml CHANGES in PHANGORN VERSION 1.99-12 NEW FEATURES o added neighborNet algorithm (Bryant and Moulton 2004) very experimental at the moment BUG FIXES o plotBS was not working correctly if bootstraped trees are in compressed form (bug report by Tobias Müller) OTHER CHANGES o many splits and networx methods have been improved and a vignette was added o phangorn now suggests only the rgl and not depends on it to avoid problems on different platforms (suggestion by Matt Pennell) o new package dependencies knitr for html vignettes and nnls CHANGES in PHANGORN VERSION 1.99-10 BUG FIXES o reorder.networx may not work as expected o Gamma model was not working properly in simSeq.pml CHANGES in PHANGORN VERSION 1.99-9 BUG FIXES o bug fixes for clang environment o midpoint takes care of node labels CHANGES in PHANGORN VERSION 1.99-8 NEW FEATURES o pmlPart got an argument rooted to handle rooted trees o simSeq is now a generic function. This simplifies the construcion of parametric bootstrap test o SOWH.test (very experimental) o as.networx and plot.networx improved considerably (often generate networks less edges) and planar graphs are now plotted nicely BUG FIXES o fixed some bugs in ancestral.pars o amino acid model "Blosum62" was not working OTHER CHANGES o improvements to read.nexus.splits, write.nexus.splits to be more consistant with SplitsTree o splitsNetwork got an additional argument splits o help for consensusNet, as.splits, as.networx have been reorganised and improved o treedist is much faster for larger trees o several changes to keep R CMD check happy o a development version phangorn is now available on github https://github.com/KlausVigo/phangorn.git CHANGES in PHANGORN VERSION 1.99-6 NEW FEATURES o cladePar helps coloring trees o treedist is faster for larger trees, better documentation and examples BUG FIXES o the plot of consensusNet shows now the proper bootstrap values OTHER CHANGES o phangorn does not depend only suggest rgl (should build on OS X now) o default rearrangement for parsimony is now "SPR" CHANGES in PHANGORN VERSION 1.99-5 NEW FEATURES o RF.dist works also on "multiPhylo" objects and is quite fast o optim.pml can now handle NNI tree arrangements for rooted trees, still experimental but useful for dating etc. BUG FIXES o rNNI did return sometimes trees without tip labels o SH.test did not work for pmlCluster objects o df for rooted rooted/ultrametric trees are correctly computed OTHER CHANGES o lots of internal code C-code changed o 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) o registered C routines CHANGES in PHANGORN VERSION 1.99-0 NEW FEATURES o new function dist.p to estimate pairwise polymorphism p-distances from DNA sequences BUG FIXES o as.data.frame.phyDat returned only site patterns and so did write.phyDat for nexus files o some of the recently introduced (1.7-4) amino acid models were not known by all functions and contained NAs OTHER CHANGES o changed package imports and depends structure to aviod error messages, thanks to Brian Ripley o a lot of the internal C-code has changed CHANGES in PHANGORN VERSION 1.7-4 NEW FEATURES o densiTree plots are available now o new species tree and super tree methods o more amino acid models BUG FIXES o phangorn now depends on rgl instead of suggests rgl, rgl wants to be loaded before igraph, otherwise a compiling error on some platforms occured! o fixed a bug that sometimes caused in pratched to crash o fixed a bug when using negative indices in subset.phyDat o the search heuristic SPR in optim.parsimony evaluates now more trees and is more likely to find better ones OTHER CHANGES o underlying C-code for several functions has changed. less memory reallocations and potentially time savings hopefully I included not too many bugs o optimising edge length changed from Jacobi to Gauss-Seidel method and will hopefully be more robust in the long term! o Descendants is much faster for option type="all" o plotAnc gives user more control and produces nicer plots CHANGES in PHANGORN VERSION 1.7-1 NEW FEATURES o pmlPart got additional argument model (request from Santiago Claramunt) BUG FIXES o pmlPart should be more robust OTHER CHANGES o started reorganising the code o underlying code of several parsimony functions has changed and these are now considerably faster o some examples are changed to allow faster checking on CRAN CHANGES in PHANGORN VERSION 1.6-5 NEW FEATURES o dist.hamming handles ambigious states now as dist.ml (request from Arne Mooers) BUG FIXES o phangorn links properly to ape CHANGES in PHANGORN VERSION 1.6-3 NEW FEATURES o optim.parsimony has a new search heuristic (SPR) BUG FIXES o changed package to work with igraph >= 0.6 OTHER CHANGES o arguments of pratchet changed CHANGES in PHANGORN VERSION 1.6-0 NEW FEATURES o dist.ml has more options and is faster (ca. 5 times for nucleotides and 20 times for amino acids) BUG FIXES o plotBS did not work properly with ape version 3.0 OTHER CHANGES o vignettes changed for a faster compilation of the package o Ancestors allows a vector of nodes as input o midpoint uses less memory and works for larger trees (10000 of tips) o ancestral.pars gives better formated output CHANGES in PHANGORN VERSION 1.5-1 OTHER CHANGES o several examples changed for a faster compilation of the package CHANGES in PHANGORN VERSION 1.5-0 NEW FEATURES o codon models can be used directly (dn/ds ratio can be computed) o modelTest works now also for amino acids BUG FIXES o the code to compute RI and CI changed and should be more robust OTHER CHANGES o package parallel is used instead of multicore o vignettes, examples, help improved o ChangeLog is called NEWS CHANGES in PHANGORN VERSION 1.4-1 NEW FEATURES o parsimony branch-and-bould algorithms bab (so far pretty slow and memory intensive) o more amino acid models o function nnls.tree to compute non-negative edge weights for a given tree and a distance matrix BUG FIXES o allTrees returns now an integer edge matrix, this could have caused some problems previously o CI and RI now take better care of ambiguous states o dist.ml has default value for amino acids o as.splits.multiPhylo produces more sensible bipartitions and so lento and consensusNet produce more useful plots (thanks to Emmanuel Paradis) OTHER CHANGES o several changes to the networx classes and methods o modelTest now also returns the function calls of the estimated models, which can be used in downstream analyses o vignette "Trees" has a few more examples o dist.ml is more general (base frequencies and rate matrix can be supplied) o pml objects are more compact, thanks to the Matrix package o xtable is now a suggested package (needed for vignettes) CHANGES in PHANGORN VERSION 1.4-0 NEW FEATURES o plot.network to plot split networks in 3D (requires rgl) and 2D (still very experimantal) o consensusNet computes consensus networks o Lento plot allows to take multiPhylo objects as input BUG FIXES o CI and RI did not work with only one site pattern present o pratchet returned only one, not all of the best trees found OTHER CHANGES o phangorn now requires the Matrix, igraph and rgl packages o designTree returns a sparse Matrix and this can save a lot of memory o 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 CHANGES in PHANGORN VERSION 1.3-1 BUG FIXES o the multicore package may failed, if executed in a GUI environment, more error checks included o optim.pml, in rare cases may failed to optimize edge length (should be more robust now) OTHER CHANGES o some changes to keep R CMD check happy o modelTest, pratchet, bootstrap.pml, bootstrap.phyDat got an additional argument multicore option to switch between serial and parallel execution CHANGES in PHANGORN VERSION 1.3-0 NEW FEATURES o acctran to assign edge length to parsimony trees OTHER CHANGES o phangorn can now be cited o additional and improved ancestral reconstructions methods (ACCTRAN, MPR) o new vignette describing ancestral sequence reconstruction CHANGES in PHANGORN VERSION 1.2-0 NEW FEATURES o new function pratchet (parsimony ratchet) o new function midpoint for rooting trees o new function pruneTree to build concensus trees from node labels (e.g. bootstrap values) o multicore support for modelTest BUG FIXES o ancestral.pars sometimes did not show all possible states o the call-attributes did not get proper changed in update.pml and optim.pml OTHER CHANGES o there is now a general help page displayed with '?phangorn' o dist.hamming is faster o getClans, getSlices and getDiverstity can now handle multifurcating trees CHANGES in PHANGORN VERSION 1.1-2 NEW FEATURES o more generic methods for class splits (print, as.matrix) o plotBS can plot now cladograms and phylograms BUG FIXES o read.phyDat sometimes did not work properly for amino acids CHANGES in PHANGORN VERSION 1.1-1 NEW FEATURES o optim.pml allows to optimize rooted trees OTHER CHANGES o description of getClans improved CHANGES in PHANGORN VERSION 1.1-0 NEW FEATURES o Consistency Index (CI) and and Rentention Index (RI) o clanistic tools o new generic function cbind.phyDat o optim.parsimony works now also with the fitch algorithm, faster than the sankoff version BUG FIXES o treedist and RF.dist now check whether trees are binary and try to handle multifurcations (thanks to Jeremy Beaulieu for bug fixes) OTHER CHANGES o second vignette describing some special features o allTrees is faster o trace and pml.control are now more consistent o optim.pml uses less memory and can be faster for data with lots of characters CHANGES in PHANGORN VERSION 1.0-2 BUG FIXES o pml.control did not work properly OTHER CHANGES o pmlCluster, pmlMix and pmlPart gained an attribute control, which controls the outermost loop o some more error checking for pml and parsimony classes (thanks to Emmanuel and Liat) CHANGES in PHANGORN VERSION 1.0-1 NEW FEATURES o ancestral sequence reconstruction (parsimony and likelihood based) o a small convenience function acgt2ry for ry-coding o as.phylo.splits computes a tree from compatible splits BUG FIXES o a small error in pmlCluster was fixed OTHER CHANGES o upgma changed to accommodate change in as.phylo.hclust o lento plots are looking nicer CHANGES IN PHANGORN VERSION 1.0-0 NEW FEATURES o implementation of many nucleotide substitution models (additional general transition models can be defined) o new function modelTest, comparison of different phylogenetic model with AIC or BIC o Lento plot o subset functions for phyDat objects BUG FIXES o an error in pace is fixed OTHER CHANGES o parsimony (fitch and sankoff) can now handle multiPhylo objects o splits structure (which is a list of bipartitions), used by lento and hadamard conjugation o phyDat objects can be more general generated using a contrast matrix CHANGES IN PHANGORN VERSION 0.99-6 NEW FEATURES o pace, extracts the ancestral states of the root of a tree using the sankoff algorithm BUG FIXES o fixed a bug in dist.ml (thanks to Emmanuel) o fixed a bug introduced to SH.test in 0.99-5 OTHER CHANGES o fixed several spelling mistakes in the documentation CHANGES IN PHANGORN VERSION 0.99-5 NEW FEATURES o parallel computing via multicore (so far bootstrap.pml, bootstrap.pml profit under linux) o compute edge weights for parsimony trees BUG FIXES o optim.pml had problems when o as.character converted ?,- wrongly to NA o fitch needed binary trees as input, otherwise pscore is likely to be wrong (returns now a warning) o optim.pml had a problem with identical sequences OTHER CHANGES o optim.parsimony returns now a tree with edge weights o vignette is enhanced, I fixed some spelling mistakes and added some more examples. CHANGES IN PHANGORN VERSION 0.99-4 NEW FEATURES o new generic function unique.phyDat OTHER CHANGES o internal data format phyDat changed and data are stored more memory efficient (optim.pml and friends use less memory and may be faster) CHANGES IN PHANGORN VERSION 0.99-3 BUG FIXES o RF.dist sometimes returned wrong distances o rate parameter is now properly normalized in pml.Part and pmlCluster o simSeq had problems simulating a single character NEW FEATURES o rSPR and rNNI to simulate tree rearrangements CHANGES IN PHANGORN VERSION 0.99-2 NEW FEATURES o bootstrap.pml and bootstrap.phyDat: parametric bootstrap methods o simSeq: A new function to simulate sequence data o read.phyDat: simplifies reading in alignments o SH.test: Shimodaira-Hasegawa test o RF.dist: Robinson-Foulds distance as replacement for treedist (uses less memory and is much faster) BUG FIXES o dist.ml returned wrong variances. o as.character.phyDat, as.data.frame caused an error for alignments with only one site. OTHER CHANGES o added vignette describing how to perform some standard phylogenetic analysis with phangorn. o more functions to convert between different data formats. o NNI tree search is now general possible for partition models (pmlPart, pmlCluster) CHANGES IN PHANGORN VERSION 0.0-5 BUG FIXES o Solved a namespace problem with ape (>=2.2-3). CHANGES IN PHANGORN VERSION 0.0-4 NEW FEATURES o splitsNetwork fits a phylogenetic network using a L1 penalty. (High memory consumption) o pmlPen: A new function to estimate penalized likelihood models for sets of edge weights in mixtures or partition models. BUG FIXES o dist.ml should be more forgiving for different inputs. OTHER CHANGES o a new dataset. CHANGES IN PHANGORN VERSION 0.0-3 NEW FEATURES o amino acid models o 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) o design matrices for phylogenetic distance methods o added some functions useful for simulations (nni, allTrees) OTHER CHANGES o the data object phyDat changed slightly internally o a new dataset o read.aa to read amino acid data in phylip format based on read.dna from the ape package CHANGES IN PHANGORN VERSION 0.0-2 NEW FEATURES o more generic functions (plot.pml, update.pml) BUG FIXES o the "Fitch" algorithm in parsimony contained a bug OTHER CHANGES o pml has a cleaner interface (less parameter) o new faster parsimony analysis (more compiled C-Code) o added NAMESPACE