DNA / Molecular Biology

Primary:

• The National Center for Biotechnology Information

DNA Barcoding:

• ONTbarcoder - Pipeline for Nanopore DNA Barcoding.
• miniBarcoder - Pipeline for Nanopore DNA Barcoding.
• Metacoder - Metacoder is an R package for parsing, plotting, and manipulating large taxonomic data sets  generated from high-throughput sequencing.

Genome Wide Association Sequencing:

• PLINK - Free whole genome association analysis toolset.

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
• Phylotree - Phylogenetic tree of global human mitochondrial DNA variation
• Seqtrace - An application for viewing and processing DNA sequencing chromatograms

Primer Design/PCR tips:

• BioMath Calculator
• Design PCR Primers Site
• GeneFisher Primer Design
• New England Biolabs - Guidelines for PCR Optimization
• Oligo-Calc- Oligonucleotide Properties Calculator
• PCR- Information on PCR
• PCRLinks.com
• Solution Dilution Calculator

Restriction Enzymes/Digestion Predictions:

• REBASE: The Restriction Enzyme Database
• Webcutter

Population Genetics Simulation Software:

• Easy Pop- Program for simulating population genetic data sets.
• learnPopGen- An R package for population genetic simulation and numerical analysis.
• Population Genetics Online Simulator- Simple online simulator by Bob Sheehy (Radford University)

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

Population Genomics:

• ANGSD - Program for analysis of low-coverage whole genome sequence data

Species Delimitation:

• ABGD - Automatic Barcode Gap Discovery for primary species delimitation.
• GMYC - General Mixed Yule Coalescent.
• jMOTU- Package for clustering barcode DNA sequence data into molecular operational taxonomic units (MOTU).

BEAST Phylogenetics Package and Related Programs:

• 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:

• CIPRES Science Gateway - Gateway for running phylogenetic analyses (BEAST2, RAxML, MrBayes, etc.) on the web
• BaliPhy - Bayesian Alignment and Phylogeny Estimation Software
• Ceiba- Scalable phylogeny visualization software
• LVB - Software for reconstructing evolution with parsimony and simulated annealing
• MANTiS
• Mark Miller's Analytical Software Package
• Mesquite
• MrBayes: Bayesian Inference of Phylogeny
• PHYLIP (Phylogenetics Inference Package) - Powerful phylogenetics package
• Joe Felsenstein's List of Phylogenetics Software
• MEGA - Very nice and user friendly phylogenetics software
• RevBayes - Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language
• TreeRot
• Tree Time Program for calculating evolutionary times of divergence between clades

Phylogenetics eBooks:

• Phylogenetic Comparative Methods book by Luke J. Harmon

Haplotype/Network Mapping Software:

• Network (from Fluxus Engineering)
• PopART (Population Analysis with Reticulate Trees)

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:

• University of Arizona Genetics Core
• Davis Sequencing Facility
• GENOSEQ- Genomics Facility at UCLA
• SUNY Stony Brook DNA Sequencing Facility

Useful Commercial Sites/Programs:

• Applied Biosystems - Sells fluorescent primers for genotyping.
• New England Biolabs- Site for Restriction enzymes and other reagents for molecular biology.
• Geneious - Commercial software for genetic data analysis