:: DESCRIPTION
TPP (Trans-Proteomic Pipeline) is a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to our open mzXML format.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Methods Mol Biol. 2010;604:213-38. doi: 10.1007/978-1-60761-444-9_15.
Trans-proteomic pipeline: a pipeline for proteomic analysis.
Pedrioli PG.
:: DESCRIPTION
UniGene DLST is a simple PHP/Apache/MySQL application that downloads and maintains local copies of UniGene genome tables. The default web site displays a list of genomes available in UniGene along with their most recent build number and date. If a genome has been downloaded, the build number and download date are also displayed.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
CopyCat provides an easy and fast access to cophylogenetic analyses. It incorporates a wrapper for the program ParaFit, which conducts a statistical test for the presence of congruence between host and parasite phylogenies.
::DEVELOPER
Jan P. Meier-Kolthoff, Alexander F. Auch, Daniel H. Huson, and Markus Göker.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Jan P. Meier-Kolthoff, Alexander F. Auch, Daniel H. Huson, Markus G?ker.
COPYCAT: Co-phylogenetic Analysis tool.
Bioinformatics, 23(7):898-900, 2007.
:: DESCRIPTION
PAINT is a java application for viewing tree files. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Brief Bioinform. 2011 Sep;12(5):449-62. Epub 2011 Aug 27.
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.
Gaudet P, Livstone MS, Lewis SE, Thomas PD.
:: DESCRIPTION
UGENE is a visual environment for biomolecular research, integrating ever-growing set of bioinformatics algorithms.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
Citation
Unipro UGENE: a unified bioinformatics toolkit.
Okonechnikov K, Golosova O, Fursov M; UGENE team.
Bioinformatics. 2012 Apr 15;28(8):1166-7. doi: 10.1093/bioinformatics/bts091. Epub 2012 Feb 24.
:: DESCRIPTION
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Apr 28.
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM1, Lohse M, Usadel B.
:: DESCRIPTION
GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B
Artemis: sequence visualization and annotation.
Bioinformatics (Oxford, England) 2000;16;10;944-5
:: DESCRIPTION
exonerate is a generic tool for pairwise sequence comparison.It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
::DEVELOPER
Guy Slater
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Guy St C Slater and Ewan Birney
Automated generation of heuristics for biological sequence comparison
BMC Bioinformatics 2005, 6:31doi:10.1186/1471-2105-6-31
