SWALO
:: DESCRIPTION
SWALO is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux / Mac OsX
- Bowtie 2
:: DOWNLOAD
:: MORE INFORMATION
Tag: optimization
PIVO 2 – Phylogeny by IteratiVe Optimization
PIVO 2
:: DESCRIPTION
PIVO is a program that reconstructs ancestral gene orders on complex phylogenies. Because it uses the DCJ model, it can handle linear, circular, and multilinear genomes. PIVO is mainly targeted at reconstructing rerrangement histories of mitochondrial genomes.
:: DEVELOPER
Computational Biology @ Comenius University in Bratislava
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
- Java
:: DOWNLOAD
:: MORE INFORMATION
Citation
Albert Herencsár, Broňa Brejová .
An Improved Algorithm for Ancestral Gene Order Reconstruction.
In V. Kurkova, L. Bajer, V. Svatek, ed., Information Technologies – Applications and Theory (ITAT), number 1003 in CEUR-WS, pp. 46-53, Jasna, Slovakia, 2014.
GIFT 1.0.0 – Global Optimization-based Inference of Chemogenomic Features from Drug-Target Interactions
GIFT1.0.0
:: DESCRIPTION
GIFT is a C++ package to infer the chemogenomic features from drug-target interactions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows/ Linux
- C++ Compiler
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2015 Mar 29. pii: btv181.
Global Optimization-based Inference of Chemogenomic Features from Drug-Target Interactions.
Zu S, Chen T, Li S
ATGme – A Simple DNA Sequence Optimization tool
ATGme
:: DESCRIPTION
ATGme is an open-source web-based application which can in a first step identify rare and highly rare codons from most organisms, and secondly gives the user the possibility to optimize the sequence.
::DEVELOPER
Edward Daniel & Mirja Krause.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Web browser
:: DOWNLOAD
:: MORE INFORMATION
Citation
ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization.
Daniel E, Onwukwe GU, Wierenga RK, Quaggin SE, Vainio SJ, Krause M.
BMC Bioinformatics. 2015 Sep 21;16(1):303. doi: 10.1186/s12859-015-0743-5.
Samo 0.4.1 – Protein Structure Alignment tool based on Multiple Objective Optimization
Samo 0.4.1
:: DESCRIPTION
SAMO is a protein Structure Alignment tool based on Multiple Objective optimization.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows / Linux
:: DOWNLOAD
:: MORE INFORMATION
Citation
Luonan Chen, Ling-Yun Wu, Yong Wang, Shi-Hua Zhang and Xiang-Sun Zhang.
Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.
BMC Structural Biology, Vol. 6, 18, 2006.