MGA - Release Notes

1. MGA now runs faster on multiple sequences with many mutimatches. This is due to the fact that we implemented a chaining algorithm based on a data structure known as kd-trees. This in turn means your alignments can cover the sequences better. For example, the new version now aligns three of strains of E.coli in less than 21 minutes. Six human adenoviruses can be aligned in 142 seconds. Furthermore, using new parameters (-l 10 7 5 4) MGA is now capable of aligning 92% of the Adenoviruses in 198 seconds.
2. MGA is now capable of running arbitrary alignment tools during the last phase which closes the gaps. In particular, you can specify a script calling your favorite multiple alignment tool with appropriate arguments. See the new option -msascript. The distribution includes an example script showing how to call the program CLUSTALW.
3. In the previous release of MGA, the Linux binary and the Solaris binary produced different results, which where due to different implementations of the standard library function qsort. This inconsistency is now fixed, and both binaries produce the same output.
4. MGA now has the option to write the aligned subsequences in fasta format, so that other tools can easily process them further.