v1.1.0

1.0.0 -> 1.1.0
o Replaced C4_Model_find_*() functions using names
o Fixed DP bug with non-local models
o Added Seeder and Match modules to support multi-hspset models
o Added %tcs etc to --ryo for dumping coding sequences
o Added CodonSubmat module
o Changed WordHood to work in codon space
o Changed Intron and Phase models to support joint introns for g2g
o Fixed bug with display of selenocysteine containing alignments
o Added --annotation option for cd2g model
o Fixed bug with introns in cigar strings
o Modified configure.in to compile cleanly on solaris
o Changed to use abstract sequences (requires optimisations)
o Fixed bug with --bestn tiebreaking
o Fixed bugs with suboptimal SDP alignments
o Simplified tracebacks for SDP
o Fixed bug with adjacent phased introns
o Added --codongapopen and --codongapextend
o Added new softmasking implementation