May 252015
 

Vaa3D 2.921

:: DESCRIPTION

Vaa3D (former, V3D, 3D Visualization-Assisted Analysis) is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis.

::DEVELOPER

Peng Lab @ JANELIA of HHMI

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Vaa3D

:: MORE INFORMATION

Citation:

Peng, H., Ruan, Z., Long, F., Simpson, J.H., and Myers, E.W. (2010)
V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets,”
Nature Biotechnology, Vol. 28, No. 4, pp. 348-353, DOI: 10.1038/nbt.1612.

May 252015
 
TMAJ 3.7.1 - Tissue MicroArrays Information & Image Analysis Software

TMAJ 3.7.1 :: DESCRIPTION TMAJ is software for Tissue MicroArrays (TMA’s). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program. ::DEVELOPER JHU Tissue MicroArray Core Facility and Vision Multimedia Technologies (VMT). :: SCREENSHOTS :: REQUIREMENTS Linux / Mac OsX […]

SSalign – Secondary Structure Determination in DNA/RNA Sequences

 Alignment / BLAST 327 views Comments Off on SSalign – Secondary Structure Determination in DNA/RNA Sequences
May 242015
 
SSalign - Secondary Structure Determination in DNA/RNA Sequences

SSalign :: DESCRIPTION SSalign takes a DNA/RNA sequence and attempts to determine all local alignments a sequence can produce with itself. In addition, it resolves the little problem that aligning sequences using the standard smith-waterman approach can produce different results depending from which side the alignment matrix is filled. ::DEVELOPER Tancred Frickey :: SCREENSHOTS N/A […]

JTreeView 0.8 – Java based Phylogenetic Tree Viewer

 Phylogenetic Analysis 579 views Comments Off on JTreeView 0.8 – Java based Phylogenetic Tree Viewer
May 242015
 
JTreeView 0.8 - Java based Phylogenetic Tree Viewer

JTreeView 0.8 :: DESCRIPTION JTreeView is a basic tree viewer that lets you view, reroot, rotate nodes and edit further aspects of New Hampshire bracket format trees. ::DEVELOPER Tancred Frickey :: SCREENSHOTS :: REQUIREMENTS Linux / Windows / Mac OsX Java :: DOWNLOAD  JTreeView :: MORE INFORMATION

CLANS 20101007 – Visualize Protein Families based on Pairwise Similarity

 Protein Sequence Analysis 583 views Comments Off on CLANS 20101007 – Visualize Protein Families based on Pairwise Similarity
May 242015
 
CLANS 20101007 - Visualize Protein Families based on Pairwise Similarity

CLANS 20101007 :: DESCRIPTION CLANS (CLuster ANalysis of Sequences) is a software for visualizing protein families based on pairwise similarity. A clustering is performed based on all against all BLAST similarities and the detected groups are returned. Only BLAST similarities better than a specified cutoff are used to perform the cluster analysis. ::DEVELOPER Tancred Frickey […]

BlatView – Mapping EST’s to Genomes

 Alignment / BLAST 472 views Comments Off on BlatView – Mapping EST’s to Genomes
May 242015
 
BlatView - Mapping EST's to Genomes

BlatView :: DESCRIPTION BlatView maps results from a BLAT search on to the corresponding genome/chromosome/BAC clones. ::DEVELOPER Tancred Frickey and Georg Weiller :: SCREENSHOTS :: REQUIREMENTS Linux / Windows / Mac OsX Java :: DOWNLOAD  BlatView :: MORE INFORMATION References: Kent W.J. (2002) BLAT–the BLAST-like alignment tool. Genome Res. 12(4):656-64.

HMMAccel – Speeding up HMM-searches

 Alignment / BLAST 369 views Comments Off on HMMAccel – Speeding up HMM-searches
May 242015
 
HMMAccel - Speeding up HMM-searches

HMMAccel :: DESCRIPTION HMMAccel is a small perl scipt that combines PSIBLAST with HMM-searches and greatly increases the speed of the latter. ::DEVELOPER Tancred Frickey :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Windows / Mac OsX Perl :: DOWNLOAD  HMMAccel :: MORE INFORMATION

AlnEdit 1.0 – Fast and Memory Efficient Alignment Editor

 Alignment / BLAST 391 views Comments Off on AlnEdit 1.0 – Fast and Memory Efficient Alignment Editor
May 242015
 
AlnEdit 1.0 - Fast and Memory Efficient Alignment Editor

AlnEdit 1.0 :: DESCRIPTION AlnEdit was born from the need to manually inspect and edit multiple sequence alignments containing thousands of sequences (and not being able to find any editors being able to do that)AlnEdit is a Java program and should run mith minimal hassle on most computers. ::DEVELOPER Tancred Frickey :: SCREENSHOTS :: REQUIREMENTS […]

PhyloGenie – Automating Phylome Analysis

 Phylogenetic Analysis 349 views Comments Off on PhyloGenie – Automating Phylome Analysis
May 242015
 
PhyloGenie - Automating Phylome Analysis

PhyloGenie :: DESCRIPTION PhyloGenie is a PERL script combining the various steps necessary to producing a phylome. BLAST or PSIBLAST searches are performed for all FASTA format sequences in an input file, the HSP’s corresponding to user defined selection criteria (E-value, coverage, score per column, identity) are extracted and used as a basis for multiple […]

Mclip – Motif Detection based on Cliques of Profile-profile Alignments

 DNA / Genome Analysis 346 views Comments Off on Mclip – Motif Detection based on Cliques of Profile-profile Alignments
May 242015
 
Mclip - Motif Detection based on Cliques of Profile-profile Alignments

Mclip :: DESCRIPTION Mclip is a tool for motif-elucidation in DNA/RNA-sequences. Although there are a large number of motif-detection tools around, most require “nuisance” parameters to be specified (i.e. things you would like the program to tell you, not the other way around), such as the exact width of the motif you are searching for, […]