Stars
A method to identify and compare the syntenic satellite pairs among centromeres, utilizing satellite phylogenetic information and pairwise edit distance.
Comprehensive, detailed and interactive plots for STRUCTURE and ADMIXTURE population analysis
A small R notebook describing how plot common (aDNA) population genetics PCAs using R and the tidyverse.
A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.
Two-species genome comparison pipeline (combines minimap2/SyRI, EDTA, bedtools) to identify structural variants (inv/syn), annotate TE, and plot results in R.
Step-by-step tutorial to create synteny plots for pairs and trios of genomes using JCVI's MCScan
Fast and accurate DNASeq Variant Calling workflow composed of LUSH-toolkits
RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
scripts used to download and analyze insect assemblies from GenBank
Software for iterative genotyping design in a QTL-seq experiment
FastOMA is a scalable software package to infer orthology relationship.
A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
Testing WGD placement along a species tree using gene trees.
scripts and vignettes that accompany Lovell et al (Accepted) 2020.
clairemerot / go_enrichment
Forked from enormandeau/go_enrichmentTranscripts annotation and GO enrichment Fisher tests
A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.
Mirage is ancestral genome estimation software by considering different evolutionary patterns among gene families.
Scaffolding, annotation and evolutionary study of 30 chromosome-level Drosophila genome assemblies
Recovering genes from targeted sequence capture data
Helper scripts for processing and visualization of phylogenetics datasets
Homologizer: phasing gene copies into polyploid subgenomes
HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching