A primer to phylogenetic analysis using Phylip package
by Jarno Tuimala

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This is a web based graphical user interface to use ANN-Spec developed at EMBnet/CNB.

ANN-Spec was developed for finding un-gapped patterns in un-aligned DNA sequences. The program is primarily intended for finding transcription factor binding sites in promoter regions though it can be applied to protein sequences for the detection of conserved motifs as well.

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The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.

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The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments...

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Bioinformatics for Dummies (commercial about 30USD)
by Jean-Michel Claverie and Cédric Notredame

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BMC Bioinformatics is an open access journal publishing original peer-reviewed research articles in all aspects of computational methods used in the analysis and annotation of sequences and structures, as well as all other areas of computational biology. BMC Bioinformatics (ISSN 1471-2105) is indexed/tracked/covered by PubMed, MEDLINE, BIOSIS, CAS, Scopus, EMBASE, Thomson Scientific (ISI) and Google Scholar...

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Briefings in Bioinformatics is an international forum for researchers and educators in the life sciences. The journal publishes reviews for the users of databases and analytical tools of contemporary genetics and molecular biology and is unique in providing practical help and guidance to the non-specialist...

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CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file...

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DNA Microarray Data Analysis
by Jarno Tuimala and M. Minna Laine

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