|
|
|
DNA/MOLECULAR BIOLOGY TOOLS:
The following is a list of some of the sites related to DNA applications that I have found useful at one time or another. If you think I am missing a key site(s), please let me know. Enjoy!
Primary:
Nanopore DNA Barcoding:
- miniBarcoder - miniBarcoder pipeline for Nanopore DNA Barcoding.
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:
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
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:
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:
- 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
Last Updated May 19, 2021.