Phylogenetic Graph (PhyG) v1.2

Version 1.2 Release Notes

New Features:
Added global "keep" option for equally costly graphs (can be modified lcoally for search options e.g. swap)
Swap options : level, multitraverse:True/False, best(all,Only), betterN, splitSequential, splitParallel
Support options to swapping component of Jackknife and Bootstrap (level) similar to "swap"
Fuse and Support MaxParallel option to increase use of parallel resources, but reduces memory footprint by default
Added wildcards (*,?) to rename command
Fuse option: multitraverse:True/False

Changes:
Swap trajectory is deterministic by default, but can be changed using "atRandom".

Enhancements:
Reduced time complexity of network addition heuristics
Reduced time complexity of Goodman-Bremer support values
Improved behavior of swap(alternate)
Improved performance of fuse
Reduced default memory footprint of fuse

Bug Fixes:
Fixed issue in naive/exhaustive soft-wired network optimization procedure
Fixed issue in Goodman-Bremer sample option
Fixed issue with pdf graph output on MacOS--requires installation of Cairo renderer and upgrade of Graphviz
Changed option "reportNaive" to "reportNaiveData"
Fixed issue in "report(search)"
Fixed issue in dot/graphviz file parsing that only read one graph if multiple present
Fixed issue in random fuse pair selection
Fixed issue in "select" where graphs were topologically identical but had distinct roots

Phylogenetic Graph (PhyG) v1.1

PhyG v 1.1 improves both time efficiency and optimality efficacy of graph swap functions.

There are several new swap options (see documentation) including:
level:N -- N = 0-4 ``macro'' options for exhaustive to rapid swap searches
BestOnly, Better, BetterN, and BestAll for heuristic cost evaluation
splitParallel, splitSequential, and sortSplit to control graph splitting and rejoining functions

Phylogenetic Graph (PhyG) v1.0

Version 1.0 release of PhyG with many improvements and feature enhancements since the last beta release.

Phylogenetic Graph (PhyG) v0.1.4

Changes in v 0.1.4
-- Enhancements
Added missing Threshold to control levels of missing data in terminal taxa
Changes to parallel execution
Improved initial graph building for data sets with large amounts of missing data

--Bug fixed
Compile date in splash
Upper/lower case in wide and large sequence data

v.0.1.3

Changes in v 0.1.3
-- Enhancements
Improved TNT output with TNT legible trees
Added graph evaluation procedures (Static Approximation, Single Traversal) to randomized search
Implemented Static Approximation for networks
Parallelized output of Implied Alignment fasta/c and TNT
Improved behavior of distance and character builds with missing data

-- Bugs Fixed
Transform for non 1:1 nucleotide sequences caused seg fault
Simulated annealing and drift parameter errors for networks

v0.1.2

v0.1.2 Beta release

1. Fixes issue with empty graph throwing an error in Text output
2. Changed behavior of "search'
   a) if there are no exiting graphs, distance-based graphs are first created
   b) drift and annealing only operate on current best graphs
   PhyGraphUserManual.pdf
   Tutorials.tar.gz

Full Changelog: V0.1.2...v0.1.2

v0.1.1

v0.1.1 Beta release
PhyGraphUserManual.pdf
Tutorials.tar.gz