Captus v1.5.9

Changes to captus extract:

• The option --predict will also fill gaps that can be translated during extraction, this is useful when you are searching/extracting proteins from transcripts or CDS collections or RNA reads assembled with Captus, allowing to add intervening aminoacids found in the sample but not present in the target protein.

Changes to captusd cluster:

• When clustering CDS, Captus can now translate them on the fly and cluster them as protein sequences to find homologs (new options --translate_cds and --transtable). This allows to recover larger clusters of orthologs across greater evolutionary distances than just clustering the CDS as nucleotides. The baits are still created from the CDS in nucleotides. WARNING: The sequences will be directly translated using reading frame 1, so please verify they can be translated before using this option.
• Added options to control minimum sequence coverage during deduplication (--dedup_coverage) and during clustering (--clust_coverage).

Changes to new_targets_from_alignments:

• Paralogs can be more confidently flagged when unfiltered alignments are provided. This can aid in separating in paralogs as separate loci for future extractions.