:: DESCRIPTION
MiGaL (Multiple Graph Layer) is a software used to compare RNA secondary structure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Julien Allali , Marie-France Sagot
A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison
Software—Practice & Experience Volume 38 Issue 8, July 2008
:: DESCRIPTION
DoubleTree is an an application for comparing two trees using coupled interaction. DoubleTree is built on TaxonTree.
::DEVELOPER
Biodiversity Informatics Visualization Team, Human-Computer Interaction Lab , University of Maryland
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SequenceJuxtaposer is open-source software for browsing and comparing gene sequences, using accordion drawing.It provides an immediate view of a set of sequences that a user can navigatethrough with a few clicks of a mouse.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Tamara Munzner, James Slack, Kristian Hildebrand and Katherine St. John
SequenceJuxtaposer: Fluid Navigation for Large-Scale Sequence Comparison in Context
Proc. German Conference on Bioinformatics 2004, pp 37-42
:: DESCRIPTION
TreeJuxtaposer lets you interactively view a single tree, or compare two or more trees. The software handles all kinds of trees, including phylogenetic trees, taxonomic trees, consensus trees, dendrograms from cluster hierarchies, and others. Uses nested parentheses (Newick/New Hampshire) data format. Guaranteed visibility of marked regions provides visual landmarks. Structural differences are automatically marked, and the marked clades highlight corresponding nodes on the trees through the use of a generalization of the Robinson-Foulds distance metric. Responsive drawing for even very large trees with advanced graphics techniques.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Tamara Munzner, Francois Guimbretiere, Serdar Tasiran, Li Zhang, and Yunhong Zhou.
TreeJuxtaposer: Scalable Tree Comparison using Focus+Context with Guaranteed Visibility
Proc. SIGGRAPH 2003, published as ACM Transactions on Graphics 22(3), pages 453–462
:: DESCRIPTION
GeneTree is an experimental program for comparing gene and species trees. The program can compute the cost of embedding a gene tree within a species tree, visually display the location and number of gene duplications and losses, and search for optimal species trees.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
GeneTree for win , for Power Macintosh
:: MORE INFORMATION
Citation
R D Page
GeneTree: comparing gene and species phylogenies using reconciled trees.
Bioinformatics. 1998;14(9):819-20.
:: DESCRIPTION
GenomeComp is a tool for summarizing, parsing and visualizing the genome wide sequence comparison results derived from voluminous BLAST textual output, so as to locate the rearrangements, insertions or deletions of genome segments between species or strains.
It can be easily used to compare, parsing and visualize large genomic sequences, especially closely related genomes such as inter-species or inter-strains. In addition, it can also show other sequence features like repeat sequence distributions in one whole-genome DNA sequence by comparing the genome to itself.
::DEVELOPER
Chinese National Human Genome Center
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yang, J., Wang, J.H., Yao, Z.J., Jin, Q., Shen, Y., Chen, R.S., 2003.
GenomeComp: a visualization tool for microbial genome comparison.
J. Microbiol. Meth. 54, 423-426.
:: DESCRIPTION
CCOMP (Complex COMParison) is a simple command-line tool for comparing ligand/receptor complexes. It can also be used for calculating pairwise all-atom RMSD of slightly different protein structures, taking care of missing atoms, sequence inconsistencies, etc. CCOMP reads two files in PDB format, including both a receptor and a ligand, computes a pairwise sequence alignment of the receptor molecules, generates alpha-carbon superposition of the receptor structures according to the generated alignment, and computes individual deviations per residuum.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
W. Sicinska, P. Rotkiewicz,
“Computational analysis of the active sites in binary and ternary complexes of the vitamin D receptor,”
J. Ster. Biochem. Mol. Biol., 103 (3-5), 305-309 (2007)
:: DESCRIPTION
Venn Mapper is a program that cluster heterologous microarray data based on the number of co-occurring differentially expressed genes. The application loads microarray data (gene expression ratios) and determines which genes are up- or down-regulated by a user-defined ratio cut-off level. For each experiment, lists of differentially expressed genes are computed. Every list will be compared to every other list, and the number of co-occurring genes will be calculated. With the use of the binomial distribution, so called z-values can be assigned to the overlap found between two lists. The z-values can be directly imported into the Cluster and/or TreeView software.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
Venn Mapper for Win ; Perl Resource Code
:: MORE INFORMATION
Citation:
M. Smid ,L.C.J. Dorssers, G. Jenster, Venn Mapping: clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes, Bioinformatics (2003) 19 (16): 2065-2071.