Mauve 2.3.1 - Changelog

What's new in Mauve 2.3.1:

November 12th, 2009

New features:
· Compatibility with older versions of Mac OS X

Bugs fixed:
· SNP output now handles mixed case sequence files and gap characters
· Aligner memory usage has been streamlined, resulting in reduced memory requirements for alignments with many genomes
· Fix for bug that prevented reordering GenBank-format draft genomes on the command-line
· Fixed a crash when generating mums
· Report an error when sequences containing gaps are used as input
· Remove extra newlines in the ortholog alignment output
· Fixed an OpenJDK rectangle drawing bug

What's new in Mauve 2.3.0:

June 18th, 2009

Major new features:
· Reordering contigs of draft genomes, published as Rissman et al 2009
· Export a list of Single Nucleotide Polymorphisms present in an alignment (thanks to Meg Woolfit for the suggestion)
· Export a file listing the genome arrangement as a signed permutation
· Export a list of positionally orthologous CDS, tRNAs, or misc_RNAs (thanks to Elizabeth Skippington for the suggestion)
· Export a file containing alignments of orthologous CDS, including alignments of unannotated regions predicted to be orthologous (thanks to Sam Sheppard for the idea)

Other new features::
· On Linux it is now possible to launch Mauve from outside the Mauve directory (thx Dongying Wu)
· Option to disable drawing the mouse cursor highlighting orthologous regions so that figures for manuscripts can be rendered (thanks to Andrew Kropinski for the idea)

Bugs fixed:
· An alignment would complete successfully but the viewer would fail to load it because the alignment contained invalid data in the backbone file. This bug was very commonly encountered in 2.2.0.
· An alignment with progressiveMauve would crash with an error like "cga doesn't fit" or another error message, when run on multicore computers. This was a race condition in progressiveMauve's parallelism.

Known issues:
· Parallelism has been disabled for all supported platforms to avoid a race condition bug.

What's new in Mauve 2.2.0:

June 25th, 2008

· New menu option to disable the red contig boundary lines
· Progressive aligner sensitivity/accuracy improvements
· progressiveMauve was not sensitive enough to small rearrangements, although it did have high predictive value
· progressiveMauve was not properly extending LCBs in the 2.1.x releases
· progressiveMauve did not work on 64-bit linux (indefinite waiting message)
· Versions 2.1.x did not render vector graphics when printing to PDF or EPS
· seed families are too memory intensive and are now disabled by default
· segmentation fault (crash) on linux/mac due to a bug in c sort functions
· update check causes a stall during GUI launch when the network is inaccessible
· building from source was difficult

What's new in Mauve 2.1.1:

June 12th, 2008

Bugs fixed:
· The alignment programs mauveAligner and progressiveMauve did not work on Mac due to a missing shared library (libgomp.dylib)
· progressiveMauve would occasionally crash during alignment scoring and greedy breakpoint elimination due to a math bug
· The sequence navigator did not properly highlight feature search results when launched from the menu. It did work when launched from the toolbar binoculars button.