phyg - Phylogenetic Graph (PhyG) v1.3

Version 1.3 Release notes

New Features: Network edit refinement options : level, multitraverse:True/False Support MaxParallel option default set to "True"

Enhancements: Reduced time complexity of network edit heuristics Improved behavior of Bootstrap support calculation Improved network add and delete heuristics

Bug Fixes: Fixed issue in Swap where only best graph was being swapped when multiple graphs are present Fixed error in TNT ouput for Implied Alignemnts when "#" are present in partitioned sequences Fixed issue with transforming outgroup with upper case letters

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, 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

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 parseing that only read first graph if multiple present Fixed issue in random fuse pair selection Fixed issue in "select" where graphs were topologically identical but had distinct roots

- Haskell
Published by wardwheeler 11 months ago

phyg - 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

- Haskell
Published by wardwheeler about 1 year ago

phyg - 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

- Haskell
Published by wardwheeler over 1 year ago

phyg - Phylogenetic Graph (PhyG) v1.0

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

- Haskell
Published by wardwheeler over 1 year ago

phyg - Phylogenetic Graph (PhyG) v0.1.4

Changes in v 0.1.4 -- Enhancements Added missingThreshold 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

- Haskell
Published by wardwheeler over 2 years ago

phyg - 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

- Haskell
Published by wardwheeler over 2 years ago

phyg - 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: https://github.com/amnh/PhyG/compare/V0.1.2...v0.1.2

- Haskell
Published by wardwheeler over 2 years ago

phyg - v0.1.1

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

- Haskell
Published by wardwheeler over 2 years ago