SYNY-v0.9c

• Simplified default help message
• Added --help option => displays all command lines options
• Added --no_clus option => turns off gene cluster inferences
• Added --no_circos, no_barplot and no_heatmap options => skips the correspoding plots
• Now generates both pairwise and concatenated Circos plots; --circos all is set as default

SYNY-v0.9b

Bugfix release:

• Fixed strandedness in clusters_to_paf.pl, which caused collinearity SNAFUs in dotplots generated from the corresponding PAF files (e.g. .gap_5.paf).

SYNY-v0.9a

• Parallelized several processes (list creation, PAF metrics, barplots/dotplots/heatmaps)
• Fixed an issue with out-of-bounds links in Circos plots due to 1-based vs. 0-based PAF columns
• Standardized shell output + added progress counters

SYNY-v0.9

run_syny.pl: Circos plotting is now multithreaded (one plot per thread)
run_syny.pl: Now generates concatenated and/or pairwise circos plots with --circos cat, --circos pair, --circos plot
run_syny.pl: Changed default threads value to 16 ## Previously defaulted to 8
nucleotide_biases.pl: Now generates concatenated, pairwise and single circos configuration files

SYNY-v0.8e

• get_synteny.pl: Fixed issue with out-of-order locus_tags when inferring synteny from protein clusters
• list_maker.pl: Fixed issue with multiple isoforms sharing the same locus_tag in GenBank files
• Now generates heatmaps summarizing percentages of colinear bases between genomes (with paf_to_heatmap.py)
• Fixed title in protein cluster heatmaps
• --threads option now applies to minimap2 alignments and diamond homology searches

SYNY-v0.8d

• run_syny.pl now generates Circos plots for all requested gap values if --circos is invoked (+ moved plotting to subs).
• Moved Circos plots to CIRCOS_PLOTS/ subdirectory
• Standardized Circos / barplot / dotplot file names using the .mmap/ .gap_0 affixes
• Renamed Circos configuration filenames in the CIRCOS/ subdirectory for greater clarity

SYNY-v0.8c

• paf_to_barplot.py / paf_to_dotplot.py now load queries/subjects from fasta files => otherwise some queries/subjects are missing from PAF files when no match is found.
• Fixed relative positions in PAF files generated with clusters_to_paf.pl
• Dotplots are now generated both from minimap2 pairwise genome alignments (.mmap.) and from protein clusters found with SYNY (e.g. .gap_0.)
• Added minimap2 --threads option to run_syny.pl + set default value to 8

SYNY-v0.8b

• Fixed memory usage in paf_to_dotplot.py + added SVG output. Now runs much faster too.
• Fixed memory leak in paf_to_barplot.py
• clusters_to_paf.pl now generates PAF files from clusters identified by SYNY
• Barplots are now generated from these PAF files and are identified with the gap affix, e.g. .gap_0.
• Barplots generated from minimap2 alignments are now labelled with the .mmap. affix

SYNY-v0.8a

• Moved PAF to Circos links conversion to paf2links.pl subscript
• Added --clusters option to color ribbons in Circos plots by clusters instead of by contigs ## Useful when comparing bacterial genomes

SYNY-v0.8

• Added installation script setup_syny.pl. Tested on Fedora, Ubuntu, Debian, Kali and openSUSE Tumbleweed Linux distributions.
• Changed default heatmap palette from crest to winter_r; crest was missing from seaborn in some Linux distros...
• Fixed issue with clustered dendrograms; cm.figure.suptitle => cm.fig.suptitle; .figure.subtitle was not recognized in all distros...