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