CHANGES

VERSION 2.11.0-gv

* Fix buffer initialization in SD motif detection code.
* Fix indexing error for reverse strand in `calc_orf_gc`.
* Avoid skipping candidate RBS positions in `rbs_score`.

VERSION 2.10.0-gv

* Increase `MAX_GENES` and `MAX_SEQ`.

VERSION 2.9.0-gv

* Added two gene models for phages using the genetic code 11 to the metagenome mode.

VERSION 2.8.0-gv

* Added four gene models to the metagenome mode: three with the genetic code 11 and one with the genetic code 15.

VERSION 2.7.0-gv

* Added two gene models using the genetic code 15 to the metagenome mode.

VERSION 2.6.3-gv

* Added four NCLDV gene models to the metagenome mode.

VERSION 2.6.3

* Fixed a bug in protein translation output of partial genes where TTG/GTG
codons were being incorrectly translated to methionine.

VERSION 2.6.2

* Added support for translation table 25.
* Corrected another bug affecting MacOS.
* Fixed a line in the 'uninstall' directive in the Makefile.

VERSION 2.6.1

* Fixed a bug that mainly affected Mac compiles 7/2013 and
posted to Google Code and Github as 2.60 (bad, as we already
had a 2.60).  Re-releasing this version 8/2014 as 2.6.1,
but the source is identical to "2.60bugfix1" except for updated dates.
a more streamlined Makefile, and a new markdown README.md.
* Moved to semantic versioning (major.minor.patch) with the 8/2014
re-release.  Committed to being more rigorous about this moving
forward.

VERSION 2.60

* Minor Output Changes:  There are some output changes in this version.  See
below for more details.
* Added a confidence score to the output, representing the % likelihood the
gene is real. (conf=99.99;, etc.)
* Redid the training for metagenomic gene prediction and added more weights
and rules.  Upped the number of training files to 50.
* Eliminated the sampling phase of metagenomic prediction and replaced it with
running on all training files within a given range of GC content.
* Fixed a bug where Prodigal incorrectly reported "Piped input detected..."
when there was no piped input.
* Changed the output function not to replace header names unless the header
is empty (formerly replaced headers <4 letters in length).
* Changed the output function to report the first word of headers in GFF/
Genbank outputs as is, without checking for GFF3 characters that need to be
escaped.
* Eliminated the sequence number from the protein translation/mrna outputs.
* Fixed a bug in protein translation where N's in the nucleotide sequence
were being translated to P's instead of X's.

VERSION 2.50

* In GFF output, changed "type=ATG" to "start_type=ATG" to fix a bug where
BioPerl's GFF parser couldn't parse the Prodigal GFF output due to a conflict
with this tag.
* Fixed a problem with genes being truncated early in small contigs when they
should run off the edges.
* Fixed a problem with multiple overlapping genes running off edges.
* Reduced the number of metagenomic bins from 8 to 6, which reduces the
running time of the metagenomic program.  This was found not to lose any
significant accuracy.
* Redid the metagenomic clustering using a different methodology and wound up
with 39 training files instead of 30.
* Added rules to increase sensitivity in draft/metagenomic fragments.
* Added rules to reduce false positives of negative coding genes in metagenomic
fragments.

VERSION 2.00

* Added metagenomic genefinding routines to Prodigal, accessible via the -p
meta option.
* Substantial Output Changes:  A definition line is now printed before each set
of CDS entries, and a '//' is printed after each set of CDS.  Detailed
information is now printed in /note fields, and in the attributes field of GFF.
For more information, see the README file.
* GFF3 Support:  The GFF output is now 9 columns (gff version 3).
* Argument Change:  The '-f' option now specifies output format type (formerly
this was done by '-o').
* New Options:  -i, -o for input/output files, -p for metagenomic/single genome
modes, -d to write DNA sequence of genes to a file, -q to run quietly.
* Built multiple FASTA handling into the base program (draft_prodigal.pl
script is no longer needed).
* Changed existing rules and added new ones specifically to handle large
numbers of small contigs (and genes that run off the edges of them).
* Fixed bugs in the add_nodes function and cleaned it up.

Output is no longer in the same format as 1.0-1.20.
Some command line options have changed from 1.0-1.20.

VERSION 1.20

* Moderately improved start site prediction by adding an upstream
scoring system for the -1/-2 positions and the -15 to -45 positions.
* Added a routine to correct starts of rarer types (TTG in E. coli, etc.)
that win via every other parameter (coding, RBS, and upstream score).
* Reduced the minimum gene size for genes running off edges to 50bp.  This
should help in identifying fragmented genes in draft or metagenomic data.
* Added more detailed information to the starts file, including ATG/GTG/TTG
usage, the RBS bin and spacer distance, and the new upstream composition
score.
* Added a '-n' option to force the program not to use the SD motif finder.  
(This can be useful if you suspect the organism uses a motif like AAGAGG and 
you would like to get to the AAG/etc. motifs which will be missed by the SD 
finder.  It is also useful to get very specific RBS motifs and spacers in
the starts file).
* Added gene.c/h files containing a data structure for final gene models
(exported from the dynamic programming).  Moved printing of translations and
gene models to this data structure.
* Added GFF output specifiable with the '-o gff' option.
* Fixed a bug where running with a training file and without a training file
produced different results (this elusive bug has existed since 1.0).
* Modifed intergenic score weighting and fixed some minor bugs with this
function.
* Fixed some bugs that only occurred when compiled for Windows.
* Modified draft_prodigal.pl to catch signals and generally run more robustly.

Starts files are no longer in the same format as 1.0-1.10.
Training files for 1.0-1.10 are NOT compatible with 1.20+.

VERSION 1.10

* Added support for multiple FASTA input via a wrapper script called
"draft_prodigal".  Requires Perl 5.
* Added an alternative start scoring model that automatically discovers RBS
motifs and builds a model from upstream regions.  This model was found to
perform slightly worse in SD genomes than the existing code, and it also takes
twice as long, so we only use it when a genome is determined not to use the SD
motif.
* Fixed a bug in parsing Genbank files where the parser did not understand lines
with "[gap 100] Extend Ns" etc. in them.

Training files for 1.0-1.05 are NOT compatible with 1.10+.

VERSION 1.05

* Added support for exclusion of RNA regions from gene modeling via masking such
objects in the sequence with n's and using the '-m' option to make Prodigal
recognize them as such.

VERSION 1.04

* Modified Prodigal to allow genes to run off edges.  (User can disallow this
with the -c option).
* Allowed Prodigal to run on any size sequences if using data from a training
file.

VERSION 1.03

* Fixed a bug where Prodigal didn't handle Windows C/R's in sequence input.
* Modified the start trainer to function better in the absence (or scarcity) of
good genes to train on.

VERSION 1.02

* Added protein translation support via -a flag.
* Added full translation table support via -g flag and removed the -n option.
* Fixed a bug that caused prodigal to hang occasionally (involving 4 consecutive
overlapping genes in the dynamic programming model).

Training files for version 1.01 are NOT compatible with version 1.02+.

VERSION 1.01

* Reduced the number of false positives by fixing a bug in the
eliminate_bad_genes routine that was causing genes not to be omitted.
* Increased the accuracy of the RBS scorer slightly by creating more bins based
on distance and motifs and ordering then slightly differently.
* Fixed a bug in the dynamic programming model in zero gene cases.

Training files for version 1.0 are NOT compatible with version 1.01.