    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 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





