zol - our suite for detailed comparative analysis of related gene clusters (co-located genes; e.g. BGCs, operons, etc.) - has new color aesthetics, column ordering, & new stats from the peptides library.

It no longer screams at your eyes in 80s-style neon colors 😀

github.com/Kalan-Lab/zol

Was disappointed that a recent study highlighted a bug in zol that we resolved in April and did not affect all use cases. For more on our apology to affected users, how we had addressed it and further improved zol since, and an updated benchmarking, please check out:

github.com/raufs/gene_c...

Check out this 1 min video on using zol + cgcg for scalable visualization of evo info across 1000s of homologous gene cluster instances (e.g. BGCs, phages, plasmids, defense islands, etc.) as network graphs.

Github: github.com/Kalan-Lab/zol
Docs: github.com/Kalan-Lab/zo...

#secmet #phage #genomics

cgcg uses the amazing gravis framework for creating the visual - a massive effort by Robert Haas - and simply takes as input a directory of zol results.

Inspiration comes from the Bork lab's STRING app & various pan-genome viz software
github.com/Kalan-Lab/zol

Interested in summarizing evolutionary info from 100s to 1000s of homologous gene cluster instances (BGCs, phages, genomic islands, etc.)?

We introduce cgcg in zol v1.5.0 which squashes gene clusters into a network visual where nodes are ortholog groups & edges show gene order

#secmet #phage

What's the evolutionary landscape of BGCs in your favorite bacterial species/genus?

Find out using the new lsaBGC-Pan tool, now on Bioconda🐍:

- works for fungi & bacteria
- allows joint antiSMASH + GECCO analysis
- includes new analytical modules

github.com/Kalan-Lab/ls...

#secmet #evosky

Is your bacterial strain unique? New tools in zol let you easily check the conservation/novelty of prophages, plasmids, & BGCs in a focal sample's genome against a database of target genomes (e.g. all other genomes from the same species) #phages #plasmids #MGEs #BGCs github.com/Kalan-Lab/zol

If you discovered a novel microbial strain or species, please check out abon - a new program in the zol suite, which lets you easily check the conservation of your sample's BGC-ome (from antiSMASH & GECCO predictions) across target genomes: github.com/Kalan-Lab/zo... #secmet #bgc

New in zol v1.3.10: fai generates a XLSX spreadsheet with automatic formatting showing the closest hits of a query gene cluster in the target genomes database. This allows users to easily perform manual filtration before progressing to zol!

github.com/Kalan-Lab/zol

#secmet #bgcs #phages