get_homologues-est

Release 20170807 (v3.0.6) ships with the following bug fixes and changes:

parse_pangenome_matrix.pl -S now takes an integer to indicate the minimum occupancy requested of clusters
improved description of annotate_cluster.pl -h
increased length of sequence names in annotate_cluster.pl
added parsimony-informative sites in headers of blunt-end clusters produced by in annotate_cluster.pl -b
annotate_cluster.pl now shows unaligned cluster sequences and prints number of taxa in the alignment
annotate_cluster.pl now removes temporary files
added sub collapse_taxon_alignments to lib/phyTools.pm
added annotate_cluster.pl -c 40 to collapse alignments of sequences from same taxon
added Pfam domains to collapsed sequences
initialize compartments in parse_pangenome_matrix.pl to zero if empty before plotting (thanks Felipe Lira!)
transcripts2cdsCPP.pl & transcripts2cdsCPP.pl now print name of offending files with '+' chars
temp blastdb file closed properly in annotate_clusters.pl
corrected intergenic clusters produced with get_homologues.pl -g when using prokka-annotated GenBank files
updated get_homologues.pl -g and checked this section in the manual
extract_*_genbank subs in lib/phyTools.pm now parse LOCUS when accession is not available in GenBank files, such as those made with PROKKA