What's new in Mauve 2.4.0
Mar 28, 2015
- New features:
- Compatibility with Mac OS X 10.8+
- Mauve Assembly Metrics (publication)
- SNP output from the command line
- Permutation matrix output
- Updated visual styling of similarity plots
- Mauve Contig Mover can now run headless (command-line) with OpenJDK and Oracle JDK 7 and 8
- Bugs fixed:
- Poor performance of annotation tooltips on mouseover
- Errors reading GenBank annotation from RAST and Prokka (thanks Torsten Seemann & Matt DeMaere)
- Alignment of genomes > 2Gbp
- new OpenJDK fonts caused ugly GUI component layouts
- Build incompatibilities with modern Boost libs
- Contig N50 off-by-one error in Mauve Assembly Metrics
- Boundary condition bugs in Mauve Assembly Metrics
New in Mauve 2.3.1 (Nov 12, 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
New in Mauve 2.3.0 (Jun 18, 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.
New in Mauve 2.2.0 (Jun 25, 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
New in Mauve 2.1.1 (Jun 12, 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.