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* 3.5 (unreleased)
- Graphical model framework
+ Brownian model on *random* rooted tree.
- Misc
- Switch to c++17
- Models
- Add +mut_sel_aa for selection on amino-acids in codo models.
- Haskell machine
+ Observe lists in an efficient manner.
+ Allow sampling characters on random trees (recursive, via mfix).
- Make a unified program that computes an ATModel object.
- Do logging by computing a JSON object.
- Observe likelihood of sequences on tree
- Separate random variables from modifiables.
- Make modifiables evaluate to an initial value.
- Allow specifying modifiable structures, such as a list of modifiables.
- Allow sampling a random tree topology.
- Allow logging strings.
- Record force edges.
- Garbage-collection no longer delete steps or results.
- SPEED: inline mapping routines
- SPEED: unshare_regs: move loop over created_regs out of loop on results
- SPEED: unshare_regs: don't unshare constants and index_vars
- FIX graphviz description of graph by using HTML records.
- Docs
- Split up developer docs.
- Help
+ Display functions more compactly with `help functions`
- Handle `quote` better in terminal output.
+ Allow getting help on functions, models, and distributions.
- Tools
+ Allow reading from files wherever we take a comma-separated-list
+ alignment-info: add option to show sequence names and/or lengths.
+ extract-ancestors: new program to get specific ancestral sequences.
- trees-consensus: always write out PP.
- tree-tool: add command to remove internal node names.
- Code
+ Refactoring
- Move utility code under util/
- Split util/util.H into several other files.
- Make separate libutil and libcomputation
- Packaging
+ Distribute `draw-tree` binary on windows.
- Fixes
+ Correctly escape newick names when writing tree samples.
- Correctly handle FAIL when desugaring case expressions.
+ Make bp-analyze handle windows line endings when run from cygwin/UNIX.
- Compile without errors in C++17 mode.
+ Link to math library if available: fix build on kfreebsd
+ Avoid crash with NaN on armhf.
- Don't print out newick trees rooted at a leaf.
- Speed up tree drawing in bp-analyze.
- Correctly compute PP version of MAP and greedy trees.
* 3.4.1 (Jan 18, 2019)
- Help
+ Display functions more compactly with `help functions`
- Packaging
+ Distribute `draw-tree` binary on windows.
- Fixes
+ Correctly escape newick names when writing tree samples.
- Correctly handle FAIL when desugaring case expressions.
+ Make bp-analyze handle windows line endings when run from cygwin/UNIX.
- Compile without errors in C++17 mode.
* 3.4 (Dec 13, 2018)
- Evolutionary models
- Add Doublet alphabet for RNA stems.
- Add generic +mut_sel model modifier.
+ Add models x2, x2_sym, x2x2 for RNA stems.
+ Add RNA.m16a model for RNA stems.
- Fixes
- "--" should not become a single long dash (en-dash) in man pages.
+ Don't crash if --scale is set to a constant (e.g. --scale=1).
- Allow reading (a,b):1.0; by ignoring the root branch length.
+ Properly translate newick labels with quotes or _.
+ Don't replace W with A in observed sequences unless --set infer-ambiguous-observed=true
- Misc
- Correctly log things inside a let binding.
+ Allow selecting character ranges from a file: "sequences.fasta:100-240,300-900"
+ Rename subsample to bali-subsample (to avoid conflicts with other software).
+ Install bali-phy-pkg.
+ Make BES package work again.
+ Reorganize fields on C1.log
- Hold Numeric[k] or Doublets[DNA/RNA] alignments fixed.
- Allow writing alignments every iteration.
- tree-tool: add scaling, pruning, computing diameter, etc.
- cut-range: allow selection samples from more than 1 alignment file
- alignment-thin: clean up options and man page.
- alignment-distances: new tool, add accuracy and recall metrics.
- Only compute probability *ratios*
+ Allow recovery from initial -infinity.
- Improved mixing for [0,1] random variables.
- Graphical model framework
- Interpreted models now separate the likelihood from the prior in logged output.
- Interpreted models (e.g. LinearRegression.hs) are now a lot faster.
- Simplify constructing loggers.
- Allow using poisson distribution.
- Haskell
- Allow "import modid ( .... )" and "import modid hiding ( .... )"
- Add Data.JSON module
- Implement quot, rem, div, mod.
- Implement -X NoImplicitPrelude
- Refactored functions out of Prelude into Data.List, etc.
- Implement layout-sensitive parsing.
- Implement pattern bindings (i.e. let (x,y) = E1 in E2)
- Implement @-patterns (i.e. x@(y,z) )
- Implement lazy patterns (i.e. ~(y,z) )
- Implement guards for functions and case.
- Allow modules with no "module Name where" clause.
- Implement running a module with --run-module
- Encode strings as (listFromString String)
- Add flags for dumping parsed, renamed, desugared, etc. code.
- [FIX] float let out of let if it reveals a constant.
* 3.3 (Aug 6, 2018)
- Fixes
- make bp-analyze able to parse output files from 3.0-beta.
- rename Goldman & Yang codon model to gy94 from incorrect yn94.
- fix run file for f81 model.
- fix incorrect LG model.
- normalize WAG and LG standard frequencies.
- Codon models
- gy94 and mg94 now have no submodels and are rate matrices.
- f1x4, f3x4, and f61 now compute named codon frequencies.
- add gy94_ext and mg94_ext for using any nucleotide rate matrix.
- add mg94k for mg94_ext[hky85]
- Triplet models
- fix up x3, x3_sym, x3x3
- add +dNdS function so we can do e.g. hky85+x3+dNdS
- Functions in models
- Add new syntax function[x,...] for specifying models.
- new functions map, zip, zipWith.
- m1a,m2a,..,m8a_test,branch-site, etc. now take functions as arguments.
- let-bind names for lambda-dependent arguments, but inside the lambda.
- Model framework
- +fe as synonym for +f[Frequencies.uniform]
- +f and +gwF now take exchange models like wag as a submodel.
- logging now returns an object that can change shape dynamically.
- function calls can now look like f[g[x],y] instead of just f[x,y]
- arguments now referenced with @arg to fix function[x,add[x,x]]
- fixes to unification and constraints.
- suppress gamma:shift and exponential:shift
- Haskell
- modules can now re-export imported modules.
- refactor module SModel into SModel.Codons, SModel.ReversibleMarkov, etc.
- remove hky85', etc now that models can call hky85 directly.
- add lazy IO
- make sampling in the Random monad lazy
- correctly set rates in sample'
- do normal 0 1 => do sample $ normal 0 1
- Docs
- Reorganize docs on substitution models.
- Move docs on partitions to new section.
- Etc
- Allow specifying alphabet for --print.
- Allow running gy94 from --print.
- Testing
- Find out why different package disagree on wag+f[wag_freq]
* 3.2 (Jun 25, 2018)
- Fixes
- Increase test timeout for internal testsuite and testiphy.
- HTML report: don't hide header behind top-bar in Chrome.
- alignment-smc improvements.
- change alignment-diff back to red
- Add NEWS file.
* 3.1.5 (Jun 13, 2018)
- Fixes
- Make all programs use shipped libstdc++
- Make MDS plots handle bp-analyze --subsample
- Increase test timeouts
- Correctly write initial alignment for fixed alignment partitions.
- Don't write "file:" for MDS URLs in HTML report
- Help
- Print citations with pmid and pmcid in help.
- Print help for 0-argument functions like 'dna'
- Improve help for fMutSel and fMutSel0
- Add Frequencies.uniform[] function.
- Make SEV handle site-compression.
- HTML report: print version number + lots of cosmetic improvements.
- Add new tool tree-tool (and map page, etc.)
- Change alignments-diff highlight color back to red.
- Clean up DP matrix code.
* 3.1.4 (Jun 9, 2018)
- Fix prior on alpha in Rates.gamma
* 3.1.3 (Jun 9, 2018)
- Fix mean_length prior in RS05 model.
- Add some more color-schemes for drawing alignments-diff output.
- Add ferns exon/intro data set.
* 3.1.2 (May 6, 2018)
- Fix a testsuite bug
- Haskell
- parse exports list
* 3.1.1 (May 5, 2018
- Fixes
- Don't require testiphy
- Print priors on models in their own section.
* 3.1 (May 2, 2018)
- Fixes
- Build alignment-thin and alignments-diff
- Show model and priors readably
- bali-phy accepted into Debian
- Change 'logp' => 'posterior'
* 3.0.2 (Mar 10, 2018)
- Docs
- man pages for bali-phy and tools
- man pages online
* 3.0.1 (Mar 6, 2018)
- Fixes
- Fix crash in alignment-thin
* 3.0 (Feb 12, 2018)
- Models
- Mixture models now work.
- MultiRate[model,dist,n_bins] also works
- let[var=E1,E2] now works
- Rename RA[a] to RevCTMC[a]
- Stop representing integer, double, and bool as strings.
- Report
- subsample trees when running trees-distances for MDS plot
- Docs
- Add help for more functions.
- Implement SPR+A
- Destroy SPR_by_NNI with fire.
* 3.0-beta6 (Jan 5, 2018)
- Fixes
- Make sorting of DP:rates and M3:omegas work again.
- sample branch lengths from prior -- fixes very long initial tree.
- specify branch lengths as a List[Double]
- Models
- Make lists into a collection of Cons[ ] functions.h
+ Speedup on 25-muscle because we aren't proposing the branch lengths badly
- Eliminate compiler warnings.
* Print expressions
- Allow non-modifiable branch lengths if we aren't doing MCMC.
- Improve pre-burnin
- read parameter values as json
- write out run parameters as json.
- Improve help, add help for more functions.
* stop finding branch lengths by parameter name
* stop finding scales by parameter name
* print parameter values that are data structures
* meson build infrastructure
* Read json using nlohmann::json
* Switch to new ptree structure.
3.0-beta5 (Dec 6, 2017)
- Fixes
- Don't crash on --smodel=GTR+x3
- Short parameter names
- Add --link option.
- Complain if linking non-existant attributes.
- Logging
* Logging of [(String,a)]
* Rationalize logging of frequencies and exchangabilities
* DirichletOn prior for frequencies and exchangabilities.
* Loading functions from files.
- Allow expressing the branch length prior in terms of the tree.
- Automatically convert integers to double when needed, and hide the conversions.
- Help
- Make simple|advanced|expert|(developer) options.
- Help for all commands.
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