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B-NET Home
Bioinformatics
Software
Datasets
Projects
NexGen Sequencing
Useful Links
Odds N Ends
National Center for Biotechnology Information
The home of GenBank, a vast amount of data and tools to use. Really, I can't say enough good things aboutt the useful programs here. BLAST, Primer Design, 2-sequence BLAST are tools I use frequently.
Bioinformatics Tools (Genscript)
Many online tools are available at this site for CRISPR, PCR primer design, siRNA work and RE analysis.
DNAStar – Commercial DNA Analysis Suite
While the complete suite is expensive, >$2,000 per year, you can subscribe to the SeqBuilder Pro for $99 (Academic License). I can’t afford the Molecular Biology Suite ($599/year) but I can afford this. I have tens of thousands of files in DNAStar proprietary formats.
ExPASy
This is a page of Bioinformatics tools. Unfortunately, it is no longer being updated but there are many, many useful programs listed here.
GeneStudio Professional
A once commercial DNA analysis suite now available for free.
Phil Green Laboratory – Genome Sciences Department, University of Washington
The home of phred, phrad and consed. These are DNA assembly algorhythms and programs. Academic institutions can get the programs for no cost.
MEGA (Molecular Evolutionary Genetics Analysis)
The home of MEGA software and a treasury of free phylogenetic and evolutionary analysis information. Alignment programs, programs to infer phylogeny and programs to draw trees demonstrating phylogeny. What’s not to love.
I've been using this program since DOS.
ImageJ
A wonderful, free image analysis program from NIH.
PARSEC
This is an online search tool for PAtteRn Search and Contextualization (PARSEC). You submit your sequences
PHYLIP
More free phylogeny software, updated to 64-bit code.
Some of the original phylogeny software.
Phylogeny Programs organized by method and system
A massive table of phylogeny programs listed by operating system, Unix, Windows, Mac, or Linux.
Primo Primer Design
Online primer design and analysis. You need to have Java installed to use this.
ReadXplorer
This is free software for evaluating Next Generation Sequencing data. There is an English version of the site but it wouldn’t hurt to be able to read German.
SeaView
SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. You can use it to align sequences, infer phylogeny and draw trees. It runs on Windows, Mac and Linux systems.
SeqTools
This is a suite of analysis tools for nucleic acids and proteins. It is free for students.
Sequence Read Archives (SRA) at NIH
Sequence Read Archive (SRA) makes biological sequence data available to the research community to enhance reproducibility and allow for new discoveries by comparing data sets.
Sanger Center – Search Tools and Software
This is a collection of open access software for a variety of biological models. There are many sequencing and DNA analysis programs available.
Vista
This U of CA site hosts a variety of comparative genomics programs.
Wikipedia Bioinformatics Tools Page
Wikipedia has a table of open source bioinformatics tools that run under a variety of operating systems.
