Recent Releases of PhyloNetworks
PhyloNetworks - v1.2.0
PhyloNetworks v1.2.0
new features: - readphylip - new options to control edge lengths in breakedge!
(These options may be used in a future release to control where the root is placed when re-rooting a network, or where a new edge is grafted when adding a new leaf.)
Merged pull requests: - v1.2.0: readphylip, breakedge! options back-compatible (#235) (@cecileane)
Closed issues: - performance improvement: network moves (#8) - writeTableCF not defined (#233)
- Julia
Published by github-actions[bot] 7 months ago
PhyloNetworks - v1.1.0
PhyloNetworks v1.1.0
New features: - expected f-statistics - μ-distance between networks - construction of a network's tree of blobs
Bug fix / enhancement: - allow for + in scientific notation when parsing a network's newick description
Merged pull requests: - feat: handle plus sign in scientific notation floats (#223) (@cvigilv) - Importing tutorial material from the wiki (#225) (@jjustison) - Fix links to google groups (#226) (@jjustison) - expected f-statistics (#227) (@cecileane) - Mu representation (#229) (@ayusharma17) - tree of blobs (#231) (@cecileane)
Closed issues: - The new version of the software has some errors. (#220) - readnewick and empty taxon names (#222) - Quartet MaxCut not available; alternative species tree methods (#224) - Wrong root (#228) - clade not appearing in BSc (hybridclades_support) (#230)
- Julia
Published by github-actions[bot] 9 months ago
PhyloNetworks - v1.0.0
PhyloNetworks v1.0.0
PhyloNetworks v1.0.0 is a major change from version v0.16.4, to serve as a "core" for the manipulation of phylogenies, used by other packages with more specialized functionalities. - many functionalities were moved to other packages (e.g. SNaQ.jl and PhyloTraits.jl) - new core functionalities are available.
Merged pull requests: - tagbot fix; new: getlevel, istreechild, isgalled (#219) (@cecileane) - v1.0.0 (#221) (@cecileane)
- Julia
Published by github-actions[bot] about 1 year ago
PhyloNetworks - v0.17.0
PhyloNetworks v0.17.0
major changes to lighten PhyloNetworks to make it a better "core". new features include: traversal routines, getting node heights, check for time-consistency
breaking changes include:
* snaq! moved to new package SNaQ.jl
* phylolm moved to new package PhyloTraits.jl
* many function names and internal field names were modified -- older exported names are deprecated
* function to search for most parsimony network left in (not exported), but not working (was limited to level-1 networks)
* phylinc moved to new package: PhyLiNC.jl
- Julia
Published by cecileane over 1 year ago
PhyloNetworks - v0.16.4
PhyloNetworks v0.16.4
- breaking change to internal function: addleaf! returns new leaf, not net
- modified RNG within snaq!: will generate different network proposals, compared to same seed but v0.16.3
Merged pull requests: - fix bug: when deleting a hybrid edge leads to simplification of parallel edges at hybrid with 2 children (#207) (@cecileane) - Fix for the slow but constant increase in memory usage (#209) (@NathanKolbow) - fix 2-cycle (parallel edges) bug in snaq (#211) (@cecileane) - documentation: workflow, badges, workshop link, ftest warnings (#212) (@cecileane)
Closed issues: - MrBayer error (#208) - 2-cycle (parallel edges) proposed in SNaQ (#210)
- Julia
Published by github-actions[bot] over 1 year ago
PhyloNetworks - v0.16.3
PhyloNetworks v0.16.3
Merged pull requests: - CompatHelper: bump compat for NLopt to 1, (keep existing compat) (#202) (@github-actions[bot]) - fix #201 and #205 (#206) (@cecileane)
Closed issues:
- infinite loop in readTopologyLevel1 (#201)
- Feedback on Detected EXCEPTION-HANDLING (#203)
- The confusion of starting topology (#204)
- fitdiscrete error with new String7 from CSV (#205)
- Julia
Published by github-actions[bot] over 2 years ago
PhyloNetworks - v0.16.2
PhyloNetworks v0.16.2
Closed issues:
- Get rid of TableRegressionModel (#185)
- Support extended Newick? (#193)
- Inheritance Probability Confidence Interval? (#198)
Merged pull requests: - CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat) (#199) (@github-actions[bot]) - for v0.16.2 (#200) (@cecileane)
- Julia
Published by github-actions[bot] almost 3 years ago
PhyloNetworks - v0.16.1
PhyloNetworks v0.16.1
- better method to read a 'trees' block from a nexus-formatted file
writeTableCFmore generally applicable to convert a vector ofQuartetTs to a data frame
Merged pull requests: - read nexus tree blocks: with translate tables and networks (#197) (@cecileane)
- Julia
Published by github-actions[bot] almost 3 years ago
PhyloNetworks - v0.16.0
PhyloNetworks v0.16.0
breaking changes: - Getter names (getchild, getparent etc.) were changed with standardized names, and are now exported. Old getter names are deprecated, so users should run julia with deprecation warnings (julia --depwarn=yes) to get info on new names to update their code. - PhyloNetworkLinearModel's are no longer wrapped in a TableRegressionModel - Evolutionary model of TraitSimulation and PhyloNetworkLinearModel objects: now in field 'evomodel'
new: - more accessors, e.g. getroot, isleaf, isexternal, isrootof, isparentof, ischildof
bug fixes: - in get and setGammas: fixed to work with non-tree-child networks - in addAlternativeHybridizations!
Closed issues: - performance suggestion make trees more type stable (#155) - Ghost introgression (#192)
Merged pull requests:
- CompatHelper: bump compat for Functors to 0.4, (keep existing compat) (#189) (@github-actions[bot])
- standardize and export getter names (#190) (@cecileane)
- Get rid of Tableregressionmodel (#194) (@pbastide)
- CompatHelper: bump compat for StatsModels to 0.7, (keep existing compat) (#195) (@github-actions[bot])
- near v0.16.0 (#196) (@cecileane)
- Julia
Published by github-actions[bot] almost 3 years ago
PhyloNetworks - v0.15.3
PhyloNetworks v0.15.3
Edge type: parametrized by its Node type to use a vector of concrete type Improved manual & tests about multiple alleles
bug fixes:
removal of degree-2 nodes, used in deleteleaf! removal of hybrid edges with low inheritance read table of qCFs: bug due to compatibility; now requires DataFrames v1.3
Closed issues: - multiple alleles: bug in mapAllelesCFtable? (#143)
Merged pull requests: - better handling of 2-cycle at the root (#186) (@cecileane) - parametric EdgeT with vector of concrete node type (#187) (@cecileane) - bug fix to read table of qCFs (#188) (@cecileane)
- Julia
Published by github-actions[bot] over 3 years ago
PhyloNetworks - v0.15.2
PhyloNetworks v0.15.2
new features:
- shrinkedge! e.g. to create a polytomy
- least stable ancestor: find it, delete what's above
bug fixes in:
- rootatnode!: redirect edges before error, if re-rooting failed (and better error message, keyword argument 'verbose' removed)
- biconnectedComponents, when there were parallel edges
Merged pull requests: - bug fix for biconnected components (#182) (@cecileane) - CompatHelper: bump compat for FASTX to 2, (keep existing compat) (#183) (@github-actions[bot]) - v0.15.2: redirect edges if re-rooting failed. new: shrinkedge! (#184) (@cecileane)
- Julia
Published by github-actions[bot] over 3 years ago
PhyloNetworks - v0.15.1
PhyloNetworks v0.15.1
Merged pull requests: - CompatHelper: bump compat for Functors to 0.3, (keep existing compat) (#178) (@github-actions[bot]) - Error when the network has negative or missing branches for phylolm (#180) (@pbastide) - removedegree2nodes! : option to keep the root (#181) (@cecileane)
- Julia
Published by github-actions[bot] over 3 years ago
PhyloNetworks - v0.15.0
PhyloNetworks v0.15.0
new features in newick network parsing: - faster reading of multiple phylogenies - negative edge lengths are now read, but set to 0 - nexus-style comments are allowed (and ignored)
breaking change: - nulldeviance considers the null model without an intercept if the input model doesn't have one.
bug fixes in: - reading of fasta files, with ambiguous sites - deleteleaf! for highly non-tree-child networks - hybridlambdaformat with existing original internal node names, e.g. when read as bootstrap values, that caused Hybrid-Lambda to fail silently.
Closed issues:
- deleteleaf method bug (#153)
- Minor doc typo (#166)
- PhyloNetworks prevents BioSequences package upgrade (#168)
- Speed of readMultiTopology compared to map and fmap with large amount of trees (#170)
- readTopology with negative edge lengths (#176)
Merged pull requests: - Fast read multi topology (#173) (@gaballench) - CompatHelper: bump compat for StatsFuns to 1, (keep existing compat) (#174) (@github-actions[bot]) - Update nulldeviance for models with no intercept (#175) (@pbastide) - newick parsing: handle negative edge lengths, comments (#177) (@cecileane)
- Julia
Published by github-actions[bot] over 3 years ago
PhyloNetworks - v0.14.3
PhyloNetworks v0.14.3
- plot fix in doc
- compat: julia v1.7, BioSequences v3, CSV 0.10
Merged pull requests: - CompatHelper: bump compat for BioSequences to 3, (keep existing compat) (#167) (@github-actions[bot]) - added contributing file (#171) (@crsl4) - Project.toml, not REQUIRE (#172) (@dmbates)
- Julia
Published by github-actions[bot] about 4 years ago
PhyloNetworks - v0.14.2
PhyloNetworks v0.14.2
Merged pull requests: - bug fix, for v0.14.2 (#165) (@cecileane)
- Julia
Published by github-actions[bot] over 4 years ago
PhyloNetworks - v0.14.1
PhyloNetworks v0.14.1
Closed issues: - using phylolm() with multiple records / individuals (#101) - Cannot precompile PhyloPlots (#141)
Merged pull requests: - migrate tests+doc from travis-ci to github actions (#160) (@cecileane) - CompatHelper: bump compat for "Distributions" to "0.25" (#161) (@github-actions[bot]) - CompatHelper: bump compat for "BioSymbols" to "5" (#163) (@github-actions[bot]) - CompatHelper: bump compat for CSV to 0.9, (keep existing compat) (#164) (@github-actions[bot])
- Julia
Published by github-actions[bot] over 4 years ago
PhyloNetworks - v0.14.0
PhyloNetworks v0.14.0
new features:
- continuous trait evolution:
- model for within-species variation
- REML option (now default: breaking change)
- support for julia 1.6, DataFrames 1.0
- Julia
Published by github-actions[bot] almost 5 years ago
PhyloNetworks - v0.13.0
PhyloNetworks v0.13.0
new features: - support for julia 1.5, DataFrames 0.22 etc - move to flip a hybrid edge - check that a graph is a valid semi-directed network
Closed issues: - equal rates model fitdiscrete bug (#147) - hybridBootstrapSupport error (#154)
Merged pull requests: - Minor fixes: added 2 spaces and QuartetNetwork docstring (#135) (@crsl4) - CompatHelper: bump compat for "DataStructures" to "0.18" (#137) (@github-actions[bot]) - Flip Hybrid Edge Move (#139) (@coraallensavietta) - Fix bug in backward likelihood calculation (#142) (@coraallensavietta) - Tree component functions (#145) (@jingchengx) - CompatHelper: bump compat for "Distributions" to "0.24" (#146) (@github-actions[bot]) - CompatHelper: bump compat for "CSV" to "0.8" (#149) (@github-actions[bot]) - CompatHelper: bump compat for "DataFrames" to "0.22" (#150) (@github-actions[bot]) - CompatHelper: bump compat for "StaticArrays" to "1.0" (#151) (@github-actions[bot]) - prep for v0.13.0; travis-ci.com migration; rm test broken by GLM v1.4 (#156) (@cecileane)
- Julia
Published by github-actions[bot] almost 5 years ago
PhyloNetworks - v0.12.0
PhyloNetworks v0.12.0
new features: - simulation of multivariate BM process - NNI moves on semi-directed networks
bug fixes in: - hybridlambdaformat - neighbor-joining - likelihood of discrete traits: the bug affected data with >1 trait on non-tree networks
Closed issues: - hardwiredCluster does not accept Int taxa (#39) - strange behavior of plot/writeTopology after deleteLeaf! (#84) - Problem when analyzing choice of h (#111) - Reroot conflicts (#112) - error in hybridlambdaformat (#113) - readTrees2CF does not work (#118) - wrong warning readTableCF (#120) - minor typo in documentation (#125)
Merged pull requests: - Bug fix: wrong net.node in nj! function (#105) (@jokeitei) - Nearest Neighbor Interchange Moves in PhyloNetworks (#106) (@coraallensavietta) - major bug fix for likelihood of discrete traits (#107) (@cecileane) - Moves (#109) (@coraallensavietta) - Optimize Network Wrappers (#114) (@coraallensavietta) - Install TagBot as a GitHub Action (#115) (@JuliaTagBot) - phyLiNC Bug Fixes (#117) (@coraallensavietta) - gradient-based optimization of branch lengths (#119) (@cecileane) - AddHybridEdgeLiNC Bug Fix (#121) (@coraallensavietta) - bug fixes: root and gamma NaN (#123) (@coraallensavietta) - implementing multivariate BM process (#124) (@gabehassler) - hardwiredClusterDistance fix (#127) (@coraallensavietta) - models for rate variation across sites: +I and +G+I (#128) (@cecileane) - update to DataFrames v0.21, CSV v0.7 (#131) (@cecileane) - update to BioSymbols 4.0, BioSequences 2.0, add FASTX (#132) (@cecileane) - prep for v0.12.0 (#133) (@cecileane)
- Julia
Published by github-actions[bot] over 5 years ago
PhyloNetworks - v0.11.0
new features: - neighbor-joining - faster function to extract quartets from gene trees - format for HybridLambda simulator
breaking changes: - TICR functions migrated to QuartetNetworkGoodnessFit
- Julia
Published by julia-tagbot[bot] over 6 years ago
PhyloNetworks - v0.10.0
- StatsModels v0.6 compatibility
- indexing rules from DataFrames v0.19
- REQUIRE -> Project.toml
- better phylogeny read/write (e.g. internal node names)
- fitdiscrete: better wrapper; tools for DNA substitution models & rate variation
- clean-up: test folder, getIndex -> findfirst
- Julia
Published by julia-tagbot[bot] over 6 years ago
PhyloNetworks - v0.9.0: Julia v0.7/1.0 compatibility
update to julia v0.7 & v1.0 documentation: update to Documenter v0.21
- Julia
Published by cecileane about 7 years ago
PhyloNetworks - v0.8.0: last Julia v0.6 release
likelihood-based method for the analysis of discrete trait evolution, TICR test, documentation manual expanded, option to read trees in nexus format
- Julia
Published by cecileane over 7 years ago
PhyloNetworks - v0.7.1
bug fixes, more efficient reading of data with multiple alleles, more tests, better doc
- Julia
Published by cecileane over 7 years ago
PhyloNetworks - use DataFrames 0.11, removed RCall and Gadfly dependencies
- also use Missings, CSV, StatsModels
- tools for plots and interoperability: migrated to PhyloPlots
- Julia
Published by cecileane almost 8 years ago
PhyloNetworks - PhyloNetworks v0.5.1
based on https://github.com/crsl4/PhyloNetworks.jl/commit/a5d7349d531b6fcda9610cc8a5060f49cd63447e
- Julia
Published by cecileane over 8 years ago