v2.4.0

2.3.0 -> 2.4.0
o Fixed many thread safety bugs
o Fixed bugs with large files over 4GB
o Modified client to work with multiple servers
o Fixed server to handle SIGPIPE
o Added support for FOSN input (can be files, directories or servers)
o Fixed bug with --wordambiguity and --wordjump (with normal FSM)
o Added %pS to --ryo (percent self score over equivalenced regions)

v2.3.0

2.2.0 -> 2.3.0
o Fixed several bugs with thread safety for exonerate-server
o Fixed bug with custom genetic codes not working
o Fixed bug with overflow of seedrepeat horizon in hspset
o Added passing of wordlimit params to server
o Implemented --cores option for multi-threaded alignment
o Added identity and similarity score for GFF genes and exons
o Increased default FSM memory limit to 256Mb
o Added --revcomp option to disable searching of reverse complement
o Fixed bug with compact-FSM (VFSM) based database searching
o Added --wordambiguity option for searching ambiguous reference seqs
o Fixed bug with esd2esi and .esd files >2Gb

v2.2.0

2.1.0 -> 2.2.0
o Fixed bug with esd2esi when softmasking is off
o Removed all GMemChunk usage due to caching problems with glib-2
o Fixed various minor memory leaks

v2.1.0

2.0.0 -> 2.1.0
o Fixed portability bugs for x86_64
o Added linecount: tag for long client:server messages
o Added setsockopt(TCP_NODELAY) to improved socket performance
o Changed server to use pthreads by default to avoid LSF memlimit problems
o Added faster implementation of Sequence_strncpy()
o Fixed bug with sequence caching
o Added -V 3 client-server debug code
o Prevented sub-optimial alignments below geneseed threshold from appearing
o Fixed sorting of translated indices
o Completed implementation of server-side geneseed
o Fixed bug with .esd file parsing
o Made compilation use glib2 by default
o Fixed SDP memory management bug
o Fixed segfault bug with --refine (Thanks to Don Gilbert)
o Improved splice site scoring
o Reverted to protein substition scoring for cd2g model
o Fixed bug with fasta parser and \r\n type newlines

v2.0.0

1.4.0 -> 2.0.0
o Modified exonerate to work in Client:Server mode
o Fixed --refine to work with SDP alignments
o Disabled codegen warnings from bootstrapper during compilation
o Added --geneticcode option for using alternative genetic codes
o Added --splice5 and --splice3 to allow alternative splice site PSSMs
o Fixed several bugs when scanning query sequences (eg. --forcescan query)
o Fixed to report query on forward strand whenever possible.
o Fixed --ryo sequence dumping with --bestn
o Fixed a bug with missing seeds when using --annotation
o Changed license to GPLv3
o Added protein2dna:bestfit and protein2genome:bestfit models
(works with exhaustive alignment only)

v1.4.0

1.3.0 -> 1.4.0
o Improved splice site cache memory management
o Added --geneseed option to speed up large-scale analysis
o Fixed a bug with 3'utr coordinates in GFF output
o Fixed a crash during GFF dumping when using glib2
o Added error message for failed seeks when input is stdin

v1.3.0

1.2.0 -> 1.3.0
o Fixed a bad memory leak in boundary.c
o Fixed bug with selenocysteines in query sequences
o Fixed bug with subsequence creation (and --ryo problems)
o Fixed a bug with transition mapping in reduced space alignments
o Removed variable_submat to fix bugs with codegen and allow speed ups
o Fixed bug with --usetlaaa and translated models
o Fixed emit calculation in HPair for BSDP
o Added C field to vulgar for disambiguation of codon matches
o Fixed bug with region finding in exhaustive DP codegen
o Fixed GFF bugs (start always < end) and off-by-one bug on rev strand
o Fixed bugs with codegen for cd2g
o Fixed bug with chained silent transitions in reduced space traceback
o Fixed bug broken bigseq comparisons
o Fixed --percent and --bestn ungapped comparisons

v1.2.0

1.1.0 -> 1.2.0
o Fixed bugs with SDP and short exons in spanned models
o Fixed bug with overwriting of some valid SDP span scores
o Fixed forward coordinates in GFF
o Added utr3,utr5 and cds fields to GFF output
o Fixed rounding bug in codonsubmat
(this prevented codon models working on some machines)
o Updated SDP codegen
o Fixed compilation to work with both glib-1 or glib-2
o Fixed phase macros
o Fixed build problems on OSF
o Added initial client/server code (nothing useful yet)

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

v1.0.0

0.9.1 -> 1.0.0
o Added code for sdp over spanned models
o Added initial code for UTR model
o Fixed various minor bugs
o Improved error reporting
o Added --fastasuffix option for filtering directory contents
o Made installation of utilities optional
o Fixed memory bug with --percent option
o Improved build system

0.9.0 -> 0.9.1
o Fixed memory leak with SDP
o Bug fix to handle selenocysteines
o Fixed bug with words missing from word neighbourhood
o Fixed minor bugs and altered alignment display