cyclope 0.1
:: DESCRIPTION
cyclope is a command-line tool for multiple circular sequence alignments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
:: DOWNLOAD
:: MORE INFORMATION
Tag: sequence alignment
Bayes Aligner – Bayesian Adaptive Sequence Alignment Software
Bayes Aligner
:: DESCRIPTION
Bayes Aligner is a bayesian adaptive sequence alignment algorithms.Instead of requiring a fixed set of parameter settings, this algorithm returns the Bayesian posterior probability for the number of gaps and for the scoring matrices in any series of interest. Furthermore, instead of returning the single best alignment for the chosen parameter settings, this algorithm returns the posterior distribution of all alignments considering the full range of gapping and scoring matrices selected, weighing each in proportion to its probability based on the data.
::DEVELOPER
Brown University Center for Computational Molecular Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows/Linux/Solaris sparc
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhu, J.;Liu, J.S.; Lawrence, C.E.
Bayesian adaptive sequence alignment algorithms.
Bioinformatics 14:25-39, 1998
NeoBio 1.0 pre-alpha – Sequence alignment algorithms in Java
NeoBio 1.0 pre-alpha
:: DESCRIPTION
NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.
::DEVELOPER
Sérgio Anibal de Carvalho Junior
:: SCREENSHOTS
:: REQUIREMENTS
- Windows/ Linux / Mac OsX
- JAVA
:: DOWNLOAD
:: MORE INFORMATION
NeoBio is free software, so feel free to download and use it at your own will.
ALICAO – Contact-based Sequence Alignment
ALICAO
:: DESCRIPTION
ALICAO is a program to perform contact-based sequence alignment, where the structure of the first sequence is known (template) and the sequence of the second sequence is unknown (query). A contact map is extracted from the template structure and the program aligns the two sequences by maximizing a combination of contact mutation and sequence mutation probability. The combination of structure and sequence information overall improves alignments between sequences with < 30% sequence identity.
::DEVELOPER
The Centre for Integrative Bioinformatics VU
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
:: DOWNLOAD
:: MORE INFORMATION
Citation
J. Kleinjung, J. Romein, K. Lin and J. Heringa,
Contact-based sequence alignment,
Nucleic Acids Research 32(8) (2004) 2464-2473
Friend 2.0 – Multiple Structure Visualization & Multiple Sequence Alignment
Friend 2.0
:: DESCRIPTION
Friend (Integrated FRont-END) is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structure alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
- Windows / Linux / Mac OsX
- Java
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics. 2005 Sep 15(18):3677-8.