Prodigal 2.0 Development Version Released

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dhyatt1

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Mar 6, 2010, 1:35:30 AM3/6/10

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A beta version of Prodigal 2.0 has been released at the Google Code
site (http://code.google.com/p/prodigal).

Changes included in this version:

* 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.