CHANGES in PHANGORN VERSION 1.7-3 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 optimise 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