The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria.
Also See:
Links for Genetics Analysis:
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http://www.arb-home.de/
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Conducting basic research in the field of bioinformatics. Based at the Technical University of Denmark.
http://www.cbs.dtu.dk/ -
Multiple alignment of nucleic acid and protein sequences. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results.
http://www.clustal.org/ -
Emperor is an interactive next generation tool for the analysis, visualization and understanding of high throughput microbial ecology datasets.
http://biocore.github.io/emperor/ -
The site describes and summarizes all technical aspects involved in quantitative gene expression analysis using real-time qPCR & qRT-PCR.
http://www.gene-quantification.info/ -
MLST is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet.
http://www.mlst.net/ -
pDRAW32 is being developed as a freetime hobby project. It is far from finished, but as it has reached a point where it could be helpful for many labs, it is now available to the scientific community.
http://www.acaclone.com/ -
PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).
http://evolution.genetics.washington.edu/phylip.html -
QIIME™ is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics.
http://qiime.org/ -
Qiita (canonically pronounced cheetah) is an entirely open-source microbial study management platform. It allows users to keep track of multiple studies with multiple ‘omics data. Additionally, Qiita is capable of supporting multiple analytical pipelines through a 3rd-party plugin system, allowing the user to have a single entry point for all their analyses.
http://qiita.microbio.me/ -
RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules.
http://rnaviz.sourceforge.net/ -
scikit-bio™ is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.
http://scikit-bio.org/ -
TreeView is a simple program for displaying phylogenies on Apple Macintosh and Windows PCs.
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
