v2.0.12

Fixed anticodon detection issue for archaeal tRNAs with three noncanonical introns

v2.0.11

Fixed reverse complement of IUPAC codes

v2.0.10

• Add new covariance model to detect vertebrate mt-tRNA-Cys without D-arm in armadillos and some reptiles
• Add MitoHighConfidenceFilter, a post-filtering tool, for annotating possible mitochondrial tRNA pseudogenes or extra genes due to duplication events

v2.0.9

• Added option -j or --gff for generating GFF3 output file
• Checked Infernal version compatibility
• Fixed bug on parsing tRNAscan output in legacy mode

v2.0.8

• Fixed temporary file cleanup process
• Added function declarations for eufind and trnascan to eliminate errors when building with Xcode 12

v2.0.7

• Fixed positioning when multiple noncanonical introns exist in some archaeal tRNAs that may cause incorrect isotype and anticodon annotation
• Handled mt-tRNAs in vertebrates other than mt-tRNA-Ser-GCU that are missing D-arm
• Added new genetic code file to handle mt-tRNA-Asp in marsupials that have GCC anticodon

v2.0.6

• Fixed anticodon coordinates when archaeal non-canonical intron locates next to anticodon
• Fixed tRNA coordinates when prediction is located at the edge of truncated input sequence
• Update archaeal isotype-specific covariance models with more optimal scoring for consistent isotype

v2.0.5

Fixed code for missing tRNA predictions that only occurred when predictions were located within 200bp of long stretch of Ns used to connect contigs into scaffolds of incomplete genome assemblies

v2.0.4

• Bug fixing for incorrect position of truncated tRNA-fMet in bacterial mode
• Changed isotype and anticodon to Undet/NNN when the prediction matched with the tRNA-SeC convariance model but the predicted anticodon was not TCA
• Added code to allow the use of --max option for mitochondrial search mode

v2.0.3

Added code to adjust anticodon positions for bacterial tRNA-fMet and archaeal tRNA-His when the sequences were misaligned with the models