/Vargas-Chavez_et_al_2024_Chromosome_shattering_clitellate_origins

Repository for code and files related to the manuscript Vargas-Chávez et al. 2024. A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids

Primary LanguagePep8

Chromosome shattering at the origin of Clitellata

1. Description

This repository contains the scripts and files needed to reproduce the analysis in: Vargas-Chávez et al. 2024. A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids. (under review)

2. Directories in this repository

  • Composite_gene_analyses: This directory contains the scripts needed to idenfity composite genes.
  • Gene_repertoire_evolutionary_dynamics: This directory contains the scripts and files needed to perform the gene repertoire evolutionary analysis for a set of annelids and their outgroups.
  • Hox_genes_inference: This directory contains the files and scripts needed to identify and classify Hox genes in annelids.
  • Inference_of_ancestral_linkage_groups: This directory contains the scripts needed to obtain the Oxford dotplots and the ribbon diagrams from the output of odp.
  • Transcriptomes: This directory contains the newly generated transcriptome for Hirudo medicinalis.
  • Transposable_element_satellite_DNA_and_centromere_identification_and_analysis: This directory contains the scripts needed to identify the centromeres using the transposable element coverage and to plot them along with the tandem repeats coverage along the genome.
  • Whole_genome_alignment_and_whole_genome_duplication_analysis: This directory contains the output of halStats for the whole genome alignment using progressiveCactus.