DNA / Molecular Biology

Primary:
DNA Barcoding:
  • ONTbarcoder - Pipeline for Nanopore DNA Barcoding.
  • ASHURE  - Python-based pipeline for analyzing Nanopore sequencing metabarcoding data
  • Decona - Pipeline for processing eDNA metabarcoding data from Nanopore sequences
  • ​​eDNAFlow - Processes eDNA data from raw sequences to generation of operational taxonomic units and their abundance tables
  • ​mBRAVE - Multiplex Barcode Research And Visualization Environment
  • MetaBarFlow - Workflow for processing NGS data from metabarcoding experiments
  • Metacoder - An R package for parsing, plotting, and manipulating large taxonomic data sets  generated from high-throughput sequencing
  • miniBarcoder - Pipeline for Nanopore DNA Barcoding
  • Qiime2 - An open source, community developed, next-generation microbiome bioinformatics platform

Species Delimitation:
  • ABGD - Automatic Barcode Gap Discovery for primary species delimitation
  • bPTP - a Bayesian implementation of the PTP model for species delimitation with PhyloMap for visualization
  • GMYC - General Mixed Yule Coalescent
  • jMOTU- Package for clustering barcode DNA sequence data into molecular operational taxonomic units (MOTU)

Bioinformatics Tools:
  • Anaconda - Open ecosystem for data science and AI initiatives 
  • Visual Studio Code - Streamlined code editor with support for development operations like debugging, task running, and version control
  • Positron - Next-generation data science IDE built by Posit PBC
  • MobaXterm - Enhanced terminal for Windows for remote connection to servers for genomic analysis
  • Google Colab - A free cloud-based platform that lets you write and execute Python code in your browser
  • Kaggle - A free, online community for data scientists and machine learning engineers to learn, collaborate, and share their work
  • Pro Git - Link to second edition of a free online book on using Git by Scott Chacon and Ben Straub
  • Notepad++  - Free text editor that can open very large text files. Works with large genomics files
  • Benchling - Electronic lab notebook
  • Jupyter Notebook - Python notebook for bioinformatics

Genomics:
  • ANGSD - Program for analysis of low-coverage whole genome sequence data
  • BWA - A software package for mapping DNA sequences against a large reference genome
  • Comparative Genome Viewer - NCBI online tool for comparing two genomes
  • CONDA - Package, dependency, and environment management platform - Lets you run programs in contained environments
  • FastQC - A quality control tool for high throughput sequence data.
  • Galaxy - Open source web-based platform for genomic research. Very useful!
  • Genome Data Viewer - Online tool for exploring and analyzing NCBI annotated genomes
  • Minimap2 - A versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database (faster than BWA)
  • Pilon - Genome assembly polisher. Improves draft genome assemblies and finds variation among strains, including large event detection
  • PLINK - Free whole genome association analysis toolset
  • Racon - Genome assembly polisher. Consensus module for raw de novo DNA assembly of long uncorrected reads
  • Samtools - A suite of programs for interacting with high-throughput sequencing data
  • Trimmomatic - A flexible read trimming tool for Illumina NGS data

Genome Assemblers:
  • Canu - Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing including PacBio and Nanopore
  • Miniasm - A very fast OLC-based de novo assembler for noisy long reads

RNA-seq:
  • ​A survey of best practices for RNA-seq data analysis - PDF on RNA-seq best practices
  • Salmon - Salmon is a tool for quantifying the expression of transcripts using RNA-seq data
  • RNA-Seq De novo Assembly Using Trinity - Platform for reconstructing transcriptomes from Illumina data
  • DETONATE - Tool to compute assembly quality statistics. Useful for assessing performance of different assemblies constructed from the same data.
  • Transrate - Program for de-novo transcriptome assembly quality analysis. Statistics are comparable across assemblies
  • TransDecoder - Program that identifies candidate coding regions within transcript sequences
  • Diamond - A sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data
  • STAR - Spliced Transcripts Alignment to a Reference
  • DESeq - Differential expression analysis for sequence count data
  • RUVSeq - Normalization of RNA-seq data using factor analysis of control genes or samples
  • pheatmap - Pretty Heatmaps R package. Implementation of heatmaps that offers more control over dimensions and appearance

Functional Annotation:
DNA Sequence Alignments:
  • Blast (Part of the NCBI website; Primarily intended for sequence searches but also allows you to align two sequences).
  • MUSCLE - Online tool for Multiple Sequence Alignment.

DNA Sequence Editors/Chromatogram-DNA Visualization:
  • BioEdit - Nice program for editing DNA sequences
  • Chromas Lite - Program for editing DNA sequence chromatograms
  • Convert - Program for converting between common data formats
  • Geneious - Commercial program for DNA sequence editing and analysis - Very useful!
  • Phylotree - Phylogenetic tree of global human mitochondrial DNA variation
  • Seqtrace - An application for viewing and processing DNA sequencing chromatograms

Primer Design/PCR tips:
Restriction Enzymes/Digestion Predictions:
Population Genetics Simulation Software:
Population Genetics/Structure Software:
  • Arlequin 3.11 - Comprehensive population genetics software
  • BAPS- Bayesian Analysis of Population Structure
  • CLUMPP - Cluster Matching and Permutation Program - Used to analyze independent runs of clustering programs like Structure.
  • Distruct - Program for the graphical display of output produced by Structure
  • DnaSP - A software package for the analysis of DNA polymorphisms
  • FSTAT
  • Geneland - Program to detect population structure from allele frequencies
  • Genepop - Vey nice web program for basic population genetics analysis
  • Microsat
  • Migrate-N - Estimates Ne and gene flow using the coalescent
  • NeESTIMATOR - Program for estimating effective population size (Ne)
  • PASSaGE - Software for geographical genetics and spatial analysis
  • Structure - Powerful software for determing population structure

BEAST Phylogenetics Package and Related Programs:
  • BEAST2 - Bayesian Evolutionary Analysis By Sampling Trees 2.
  • Taming the BEAST - Tutorials for using BEAST 2.
  • BEAST- Bayesian Evolutionary Analysis Sampling Trees.
  • BEAGLE - Program that performs Bayesian calculations needed to run BEAST.
  • Tracer - Program for examining MCMC trace files produced by BEAST.
  • FigTree - Program for creating graphic phylogenetic trees from BEAST output.

Other Phylogenetics Programs:
Phylogenetics eBooks:
Haplotype/Network Mapping Software:

Microsatellite Scoring/Identification Tools:
  • MSATCOMMANDER - Software for locating microsatellites from genome data
  • Peak Scanner 1.0 - Software for sizing DNA fragments from ThermoFisher Scientific
  • STRand - Software from UC Davis for scoring microsatellites from chromatograms

DNA Sequencing/Microsatellite Scoring/Genomics Facilities:
Useful Commercial Sites/Programs:
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