:: DESCRIPTION
SRS 3D is a system for displaying 3D structures integrated with sequences and features.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Seán I. O’Donoghue, Joachim E. W. Meyer, Andrea Schafferhans and Karsten Fries
The SRS 3D module: integrating structures, sequences and features
Bioinformatics (2004) 20 (15): 2476-2478.
:: DESCRIPTION
Ampred server predicts the Antimicrobial activity of given sequence. The activity may be antifungal, antiviral and antibacterial .This server works based on Multidimensional signatures of antimicrobial peptides
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
no (only web service)
:: MORE INFORMATION
:: DESCRIPTION
GeneStudio™ Pro is a modern suite of molecular biology applications for the Windows platform built on sequence format conversion engine, SeqVerter?. All manipulations with sequences of different formats are thus seamless and transparent for the user. In addition, GeneStudio™ Pro is very well integrated with the information available for molecular biologists on the Internet
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments. Many software packages for sequence alignment and the construction of evolutionary trees have implemented their own standard of saving and reading sequence alignments. To circumvent the labourious work of manually converting alignment formats with the use of a word processor, this program was written: it converts these formats automatically.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Raes, J. and Van de Peer,Y. (1999)
ForCon : a software tool for the conversion of sequence alignments.
EMBnet.news 6(1).
:: DESCRIPTION
ANCESCON is a package for distance-based phylogenetic inference and reconstruction of ancestral protein sequences that takes into account the observed variation of evolutionary rates between positions that more precisely describes the evolution of protein families.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
W.Cai, J.Pei, and N.V.Grishin (2004)
“Reconstruction of ancestral protein sequences and its applications“.
BMC Evolutionary Biology 4(1): 33
:: DESCRIPTION
GS De Novo Assembler (Newbler) is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Science, a Roche diagnostic.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
IRiS produces a subARG in two phases by given a collection of haplotypes. A combinatorial algorithm called the DSR is a model-based approach to detecting recombinations in haplotypes (with a guaranteed approximation factor). The algorithm is based on iteratively classifying sets of lineages as dominant, subdominant or recombinant (DSR). In the first phase, DSR is run multiple times with different sets of parameters and statistical consensus is derived from them to produce a matrix of recombination information called the recomatrix. This encodes the local topology information of only the high confidence recombination events detected in the first phase. The subARG is constructed from the recomatrix in the second phase
::DEVELOPER
IBM Computational Biology Center
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Javed, A., Pybus, M., Melé, M., Utro, F., Bertranpetit, J., Calafell, F., and Parida, L.,
IRiS: Construction of ARG network at genomic scales,
Bioinformatics (2011) 27 (17): 2448-2450.
:: DESCRIPTION
Swelfe is a program that enables you to find internal repeats in DNA sequences, amino-acid sequences or 3D structures.
::DEVELOPER
RPBS(Ressource Parisienne en BioInformatique Structurale)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Anne-Laure Abraham; Eduardo P. C. Rocha; Joel Pothier
Swelfe : a detector of internal repeats in sequences and structures
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn234
:: DESCRIPTION
Taxnameconvert is a commandline software that takes as input a file with a name table and usually a Newick formatted tree file or fasta sequence/alignment file, but can also be used to exchange names in many other text file formats.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SVA is a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Ge,Ruzzo, Shianna,He,Pelak, Heinzen, Need, Cirulli, Maia, Dickson, Zhu,Singh, Allen, Goldstein (2011),
“SVA: software for annotating and visualizing sequenced human genomes“,
Bioinformatics, 27:1998-2000