EVOLUTION. ICHTHYOLOGY. CONSERVATION.
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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
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  • Home
  • Research
    • Lab Data
  • Freshw Fish West Ecu
  • Publications
  • Protocols
  • Tutorials & Code
  • People
  • Lab Pictures
  • Courses
  • Links
    • Biological Organizations
    • DePaul/Local Links
    • DNA/Molecular Biology
    • Ecuador / Latin America
    • Fish Links
    • Funding
    • Miscellaneous
    • Morphometrics/Statistics/Programming