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Paul Stothard's Projects

cgview icon cgview

CGView is a Java package for generating high-quality, zoomable maps of circular genomes.

cgview_comparison_tool icon cgview_comparison_tool

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.

document-builder icon document-builder

Produces nicely formatted PDF and HTML documents from Markdown source files.

fast-pptx icon fast-pptx

Generate Markdown and PowerPoint slides from a folder of images, code snippets, and other files.

genotype_conversion_file_builder icon genotype_conversion_file_builder

A pipeline for determining the genomic location and transformation rules for the variants described in Illumina or Affymetrix genotype panel manifest files.

helpful_commands icon helpful_commands

Command-line tools, commands, and code snippets for performing routine data processing and bioinformatics tasks.

helpful_links icon helpful_links

Links to resources related to bioinformatics and data analysis.

ncbi_search icon ncbi_search

This script uses NCBI's Entrez Programming Utilities to perform searches of NCBI databases. This script can return either the complete database records, or the IDs of the records.

seq_to_json icon seq_to_json

Converts a raw, FASTA, GenBank, or EMBL file to a JSON file. Feature information is included in the output from GenBank and EMBL files.

sequence_manipulation_suite icon sequence_manipulation_suite

A collection of simple JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. The Sequence Manipulation Suite is commonly used by molecular biologists, for teaching purposes, and for program and algorithm testing.

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