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DAGchainer logo

The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts for the distance between neighboring genes on each DNA molecule and the BLAST E-value score between homologs, maximally scoring chains of ordered gene pairs are computed and reported. This algorithm can be used to mine large evolutionary conserved regions of genomes between two organisms. Alternatively, by examining colinear sets of homologous genes found within a single genome, segmental genome duplications can be revealed. This software distribution includes both the DAGchainer utility and a Java-based graphical interface that allows the inputs and outputs to be navigated and interrogated dynamically. Registration not required.

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Published on 2010-10-26 14:53:44
Lucy DNA sequence quality and vector trimming tool logo
From SourceForge

Lucy was designed and written at The Institute for Genomic Research (TIGR, now the J. Craig Venter Institute), and it has been used here for several years to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses. The quality trimming portion of lucy makes use of phred quality scores, such as those produced by many automated sequencers based on the Sanger sequencing method. As such, lucy’s quality trimming may not be appropriate for sequence data produced by some of the new “next-generation” sequencers. Lucy is available in the form of a software download only. I currently have no plans to create an open-source community development project for lucy. If you think that would be valuable, please contact me about it. In the meantime, the download package includes the full source code, so feel free to customize it for your environment. Registration not required.

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Published on 2010-10-26 14:46:50
Elvira logo

Elvira is a set of tools and procedures designed for high throughput assembly of small genomes such as viruses. The name Elvira stands for Executive for Large-scale VIRal Assembly. Elvira is particularly suitable in situations where any of the following occur: 1. Sequences must be individually trimmed against specific primers. 2. Sequences must be trimmed against degenerate primers. 3. Assemblies need to be explicitly partitioned based on sequence origin. The Elvira package includes some well-known components, including 1. Elvira, the genome assembly pipeline for unix. 2. Lemur, the element tracking and manipulation web app. 3. GLK, the database schema and associated perl module. This software was developed at TIGR where it contributed to the sequencing and publication of thousands of viral genomes. This software makes use of the AMOS package of genome assembly tools. This software uses perl, PHP, and AJAX. Registration not required.

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Published on 2010-10-26 14:31:10
DNA Barcode Deconvolution logo
From SourceForge

This is a software library to run the JCVI barcode deconvolution pipeline using Sun Grid Engine, or optionally without the use of a grid. Registration not required.

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Published on 2010-10-26 14:30:29
Celera Assembler logo
Long sequences assembling from SourceForge

Celera Assembler : scientific software for biological research. Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing. It' a whole genome assembler originally developed at Celera Genomics for the assembly of the human genome. CeleraAssembler is now an open-source project at SourceForge. The code is actively maintained by researchers at CBCB and the Venter Institute (formerly known as TIGR, The Institute for Genomic Research). Registration not required.

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Published on 2010-10-26 14:28:35
Glimmer logo

Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. Registration not required.

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Published on 2010-10-25 15:03:26
The R Project for Statistical Computing logo

R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. R is developed by Robert Gentleman and Ross Ihaka. Registration not required.

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Published on 2010-10-22 12:01:49
Contingency Table for Ordinal Categories logo
Subcategories: StatPages

This screen computes several statistics from a table whose row and column categories form logically ordered sequences. It can accommodate a table with up to five rows and/or five columns Registration not required.

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Published on 2010-10-22 11:22:14
2 x 2 Table Analysis logo
Subcategories: StatPages

This page computes various statistics from a 2-by-2 table. It will calculate the Yates-corrected chi-square, the Mantel-Haenszel chi-square, the Fisher Exact Test, and other indices relevant to various special kinds of 2-by-2 tables. Registration not required.

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Published on 2010-10-21 12:41:47
Statistical free software logo

This page contains links to free software packages that you can download and install on your computer for stand-alone (offline, non-Internet) computing. Registration not required.

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Published on 2010-10-21 12:35:58
MAGIC Tool logo
MicroArray Genome Imaging and Clustering Tool (MAGIC Tool)

MAGIC Tool is an integrated microarray data analysis free software with open source. Registration not required.

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Published on 2010-10-21 12:23:27
visANT logo
Integrative Visual Analysis Tool

VisANT (from Bosto Univeristy) is a lightweight network visualization tool able to run as a browser-based applet or as a standalone Java program. Registration not required.

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Published on 2010-10-21 11:52:08
CellProfiler & Analyst logo
CellProfiler & Analyst allows: Image analysis

CellProfiler is a free open-source software for high-throughput image-based cell profiling using fluorescence microscopy. It is designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. CellProfiler Analyst is free open-source software for exploring and analyzing large, high-dimensional image-derived data. It includes machine learning tools for identifying complex and subtle phenotypes. Registration not required.

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Published on 2010-10-20 12:04:41
Proteopedia logo
Proteopedia allows: Weizmann

Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, it is possible edit pages in Proteopedia. Registration not required.

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Published on 2010-10-20 11:45:36
SMS Sequence Manipulation Suite logo

The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing. Registration not required.

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Published on 2010-10-20 11:08:14
JaMBW 1.1 logo

JaMBW, the Java based Molecular Biologist's Workbench, is an online platform that had been put together in order to try to give a free access to the exploitment of the most common bioinformatic operations that a molecular biologist currently has. The peculiar aspect of JaMBW, however, is to take advantage of the foremost developments in computer science in order to deliver information in a way simple to use. Registration not required.

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Published on 2010-10-19 12:40:33
Cyflogic logo
Flow cytometry software
Category: Other software

Cyflogic is a flow cytometry data analysis tool for Microsoft Windows enviroment. It has all regular analysis capabilities, such as dot plot, histogram and statistics. Registration required.

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Published on 2010-10-19 12:34:14
geWorkbench logo

geWorkbench (for genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications Registration not required.

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Published on 2010-10-19 12:30:56
ImageJ logo
ImageJ allows: Image analysis

ImageJ from NIH is the most diffused public domain Java image processing program suitable for several scientific applications. Registration not required.

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Published on 2010-10-19 12:28:16
CellDesigner logo

CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. CellDesigner is implemented in Java and thus supports various operating systems. Registration not required.

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Published on 2010-10-19 11:55:29
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