Gene-Analysis-Tools

This repository contains a collection of scripts for genomic data analysis.

Contents

• color_iTOL/
  Scripts for generating iTOL (Interactive Tree of Life) visualization files with automatic taxonomic coloring and labels. Includes batch processing capabilities for multiple phylogenetic trees. See color_iTOL/README.md for usage and details.

• extract_genbank Extract a region from GenBank files based on a table of gene pairs and accession numbers.
  For each gene pair, it finds the two reference genes in the GenBank file, extracts all features between them (inclusive), plus two genes upstream and two downstream (if available), and writes the region to a new GenBank file. See extract_genbank/README.md for usage and details.

• extract_seq/
  Perl scripts to extract sequences based on a list from a FASTA file. It contains two scripts: one to extract the sequences present in a reference list and another to extract the sequences not present in a reference list. See extract_seq/README.md for usage and details.

• pfam_filtering/
  PFAM domain filtering tools. See pfam_filtering/README.md for usage and details.

• presence_absence_heat_map/
  Gene presence/absence analysis and heatmap scripts. See presence_absence_heat_map/README.md.

• taxonomy_script/
  Taxonomy retrieval scripts using NCBI Taxonomy. See taxonomy_script/README.md.

License

This project is for non-commercial use.
See LICENSE for details.