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KeyGene Quantar Suite, TOPD/FMTS, Optimizer, Protein Clusters, PrimerPy, Fast Search and Transfer’s FAST ESP

Keygene Products has announced the release of its new genotyping software suite, KeyGene Quantar Suite, a successor to its AFLP-Quantar Pro software. The new software detects, quantifies, scores, and genotypes signals. The suite supports fragment detection-based marker technologies on all major detection platforms. It supports slab gel formats for instruments from LI-COR, FujiFilm, Molecular Dynamics/GE, as well as trace file formats for capillary electrophoresis platforms from Applied Biosystems and others.

The Evolutionary Genomics Group in the Biochemistry and Biotechnology Department of the University of Rovira i Virgily in Reus, Spain, and the Bioinformatics Laboratory at University of Ireland, Maynooth, have jointly released TOPD/FMTS, a software package to compare phylogenetic trees.
TOPD/FMTS can compare trees with leaf sets that either completely or partially overlap and can also be used to compare two trees, one or both of which are multigene family trees, the developers said. The debut version of TOPD/FMTS compares trees via split distance, nodal distance, degree of disagreement, common taxa, quartets, and triplets.
Each option is also complemented with a randomization analysis feature to test the null hypothesis that the similarity between two trees is not better than chance expectation.
TOPD/FMTS is openly available here

The Universitat Rovira i Virgili has also released Optimizer, a web server designed to optimize codon use of a gene by using pre-computed tables from more than 150 prokaryotic species under strong translational selection. Optimizer is focused on heterologous or homologous gene expression in bacterial hosts. 

The National Center for Biotechnology Information has released Protein Clusters, a collection of related protein clusters from the complete genomes of prokaryotes, plasmids and organelles.
The collection includes reference sequence proteins encoded by complete prokaryotic and chloroplast plasmids and genomes along with annotated information, domains, structures and external links. It also includes analysis tools such as multiple alignments, phylogenetic trees, and genomic neighborhoods.

PrimerPy, a new graphical user interface tool for QPCR primer design that is based on Primer3, is available here. PrimerPy is free and open source and runs on Python 2.0.

Invitrogen has implemented Fast Search and Transfer’s FAST ESP search technology as part of its website to improve navigation capabilities for its product catalog. The new search capability replaces Google Appliance, Invitrogen said.

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