PALADIN-1.6.0

Added

• Alignment command can now skip ORF detection and treat input sequences as transcripts (-q option)

PALADIN-1.4.6

Fixed

• Web request retries now work properly

Added

• Taxonomic ID and Lineage to UniProt report

PALADIN-1.4.5

Changed

• Changed UniProt web request batch size to 5000 entries to reduce chances of server timeout

PALADIN-1.4.4

Fixed

• Corrected issues causing compiler warnings

PALADIN-1.4.3

Changed

• Changed all web requests from HTTP to HTTPS to accommodate UniProt's new requirements

PALADIN-1.4.2

Fixed

• Corrected issue that sometimes caused PALADIN to hang when downloading data from UniProt
• Corrected ability to recover from UniProt server errors

PALADIN-1.4.1

Fixed

• Corrected truncated translation code descriptions

PALADIN-1.4.0

Added

• Option to detect ORFs/translate/align across multiple non-standard genetic codes (-z option). Details of available translation codes may be found here: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

PALADIN-1.3.2

Added

• Alignment command can now directly take a protein multi-FASTA and skip ORF detection (-p option)
• Prepare and alignment commands can now make use of a proxy server (HTTP/SOCKS) for contacting UniProt (-P option)

PALADIN-1.3.1

Added

• UniProt report now includes max mapping quality for each protein

Changed

• UniProt report floating precision now set to 5 digits