---v0.42---released on Oct 29, 2014

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Release notes for v0.42
Changes have been made in v0.42:
1. Fixed a bug in the identificatoin of multiple copies of SSU genes.
2. Fixed a bug in the identificatoin of genes located at the end of the linear sequence.

---v0.41---released on Oct 22, 2014

Release notes for v0.41
Changes have been made in v0.4:
1. The output GFF3 file has been cleaned up. The new file is free of "match_part". The GenBank file has also been cleaned up.
2. The features in the GFF3 file has been sorted.
3. Two parameters, one for core prtein-coding gene prediction and one rRNA gene prediction have been added.
4. A error message is provided if a file cannot be found.
5. The sample files have been updated.

---v0.4---released on Oct 11, 2014

Release notes for v0.4
Changes have been made in v0.4:
1. added another step for rRNA identification. Now the rRNA identification was performed in two steps, which use blat and HMMscan respectively. This enables the accurate identification of rRNA genes in the presence of highly similar reference sequence.
2. allow the identification of intronic proteins: reverse transcriptase, homing endonuclease.
3. constructed a tRNA blastable database, allow the identification of additional tRNA genes that were not found by tRNAscan.

---v0.3---released on Sep 30th, 2014

Release notes for v0.3

The following changes have been made in v0.3:
1. updated the backend databases to include more reference genomes.
2. lowered the e-value for initial blast search from 1e-20 to 1e-5.
3. added var1 and rps5 to the list of core genes.
4. added a function to find the start and end of a predicted CDS.