Tools

Each link leads to the GitHub repository for the tool.

PiP

An attempt to identify functions and gene sets (e.g. Gene Ontology terms) that underwent lineage(s)-specific modifications in gene expression/regulation among multiple species, by performing Phylogenetically-informed Profiling (PiP) of gene sets. Check the re-recorded PAG2022 talk for details.
The matrices of presence and absence of positive correlation between all pairs of species are superimposed to the species tree, for all gene sets. Variance of correlations are then ranked to find out the most significant modifications.

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Y Sun^*, D-H Oh^*, L Duan, P Ramachandran, A Bartlett, K-N Tran, G Wang, M Dassanayake, JR Dinneny (2022), Divergence in a stress regulatory network underlies differential growth control. Nat Plants doi:doi.org/10.1038/s41477-022-01139-5 (^*equal contribution)

An attempt to identify ortholog groups based on synteny/co-linearity and encode the evolutionary history of each ortholog group as the topology of Ortholog Network (OrthNet), among multiple closely related genomes.
OrthNet can (1) improve the resolution of solely sequence-based orthology inferences (e.g. OrthoFinder); (2) serve as a platform to organize and compare various -seq data for multiple species; (3) identify lineage(s)-specific events that modify ortholog copy numbers and synteny, such as duplication, transposition, deletion, and combinations of them; and more.

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D-H Oh and M Dassanayake (2019), Landscape of gene transposition-duplication within the Brassicaceae family. DNA Res 26:21-36 doi:10.1093/dnares/dsy035

Python scripts for exploring and fixing genome assembly (.fa) and annotation (.gtf).
Useful if you want to (1) remove chunks in the middle of sequences when there is a gene model annotation (.gtf); (2) for all gene models in a .gtf, rename transcript_id, gene_id, and gene_name fields; (3) cluster gene models from the same locus (i.e. isoforms) and select, for example, those coding for longest ORFs as “primary” gene models; (4) extract sequences for genomic regions (e.g. promoters); (5) find all sequence elements (defined as regex) in a genome; and more.

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