Release 1.2

• Version 1.2:
  • Made all modules compatible with Python 2.7 and Python 3.7.
  • SQL now implemented in Parse_Loci.py (up to 30x speedup!), Filter_Seqs_and_Species.py (3x speedup), and Taxon_Assessment.py (3x speedup).
  • Added output directory specification to all modules.
  • Two trimming modules now included: Trim_Alignments_Trimal.py and Trim_Alignments_Custom.py. The Trim_Alignments_Custom.py module allows finding start and stop block positions, and row-wise (internal) sliding window trimming based on divergence.
  • Added new module Filter_Fasta_by_Min_Seqs.py to filter fasta files using a minimum number of sequences.
  • Output directory structures improved for all modules.
  • Added --quiet option to Filter_Seqs_and_Species.py for less output on screen (useful when processing large numbers of loci).
  • Added option --numerical to Fasta_Get_Taxa.py to allow non-alphabetical identifiers for subspecies/trinomial name combinations. This allows museum, field, or numerical codes to be discovered.
  • Re-ordered tasks in Cluster_Blast_Extract.py to allow completion of all steps for one fasta file before moving to next fasta file in sequence.
  • Added multithreading for BLAST searches and new --bp_bridge flag for coordinate merging in Cluster_Blast_Extract.py and Reference_Blast_Extract.py.
  • Remove empty fasta files sometimes produced by Coding_Translation_Tests.py.
  • Complete code re-write for Align.py, Cluster_Blast_Extract.py, Filter_Seqs_and_Species.py, Parse_Loci.py, Taxon_Assessment.py.
  • Module Relabel_Fasta.py is now Fasta_Relabel_Seqs.py.