Category: DNA / Genome Analysis

DnaSP 5.10.01 – Analysis of Nucleotide Polymorphism from Aligned DNA Sequence Data

DnaSP 5.10.01

:: DESCRIPTION

DnaSP （DNA Sequence Polymorphism） is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.

::DEVELOPER

J. Rozas, P. Librado, J. C. Sánchez-DelBarrio, X. Messeguer and R. Rozas
Molecular Evolutionary Genetics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DnaSP

:: MORE INFORMATION

Citation

Librado, P. and Rozas, J. 2009.
DnaSP v5: A software for comprehensive analysis of DNA polymorphism data.
Bioinformatics 25: 1451-1452 | doi: 10.1093/bioinformatics/btp187.

Orphelia – Predict Genes in Metagenomic Sequencing Reads

Orphelia

:: DESCRIPTION

Orphelia is a metagenomic ORF finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin [1]. Orphelia is based on a two-stage machine learning approach that was recently introduced by our group. After the initial extraction of open reading frames (ORFs), linear discriminants are used to extract features from those ORFs. Subsequently, an artificial neural network combines the features and computes a gene probability for each ORF in a fragment. A greedy strategy computes a likely combination of high scoring ORFs with an overlap constraint.

Orphelia Online Version

::DEVELOPER

the Department of Bioinformatics of the University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Orphelia

:: MORE INFORMATION

Citation

K. J. Hoff, T. Lingner, P. Meinicke, M. Tech (2009)
Orphelia: predicting genes in metagenomic sequencing reads
Nucleic Acids Research, 37:W101-W105.

SeqCorator 2.03 – Sequence Editor & Feature Decorator

SeqCorator 2.03

:: DESCRIPTION

SeqCorator is a new type of sequence-graphics mixing tool that brings advanced graphics to the world of sequence analysis and illustration, creating an environment akin to a combination of Word and PowerPoint that understands sequence data. The integration of graphic drawing and styled text editing enables innovative ways for designing experiments, annotating sequences and features, and creating eye-catching presentations.

::DEVELOPER

NoeGen Inc.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

SeqCorator Trial

:: MORE INFORMATION

Order SeqCorator

SeqPup 0.9 – Biosequence Editor

SeqPup 0.9

:: DESCRIPTION

SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs.

::DEVELOPER

Don Gilbert at Indiana University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

SeqPup

:: MORE INFORMATION

This SeqPup program is Copyright (C) 1990-1997 by D.G. Gilbert.
All Rights are reserved.

DNAA 0.1.2 – Analysis Package for Short-read Next Generation Sequencing

DNAA 0.1.2

:: DESCRIPTION

DNAA (DNA Analysis) is an analysis package for short-read next generation sequencing. It comprises a suite of tools. Specifically, DNAA is able to find structural variation, SNP and indel variants, as well as evaluating the mapping and data quality.

::DEVELOPER

Nils Homer

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DNAA

:: MORE INFORMATION

License

GNU General Public License (GPL)

DGE-EM 1.00 – Accurate Estimation of Gene Expression Levels from DGE Sequencing Data

DGE-EM 1.00

:: DESCRIPTION

DGE-EM package can be used to infer gene expression levels from 3′-tag Digital Gene Expression (DGE) data. DGE-EM uses a novel expectation-maximization algorithm that takes into account alternative splicing isoforms and tags that map at multiple locations in the genome, and corrects for incomplete digestion and sequencing errors. Experimental results on real DGE data generated from reference RNA samples show that our algorithm outperforms commonly used estimation methods based on unique tag counting as well as estimates obtained from RNA-Seq data for the same samples. Results of a comprehensive simulation study assessing the effect of various experimental parameters suggest that further improvements in estimation accuracy could be achieved by optimizing protocol parameters such as the anchoring enzymes and digestion probability.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

DGE-EM

:: MORE INFORMATION

Citation:

M. Nicolae and I.I. Mandoiu,
Accurate Estimation of Gene Expression Levels from DGE Sequencing Data,
Invited talk, 1st Annual RECOMB Satellite Workshop on Massively Parallel Sequencing, March 26-27, 2011,

SeedMasker – Genome Masking based on High Occurrence Words

SeedMasker

:: DESCRIPTION

SeedMasker is public domain software for masking genomes based on over-represented words.

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SeedMasker

:: MORE INFORMATION

Citation

For now, please cite this URL:

http://www.drive5.com/seedmasker

 

PILER – Genomic Repeat Analysis Software

PILER-CR 1.0

:: DESCRIPTION

PILER is public domain software for analyzing repetitive DNA found in genome sequences.The PILER algorithm was developed by Bob Edgar and Gene Myers.

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

PILER-CR Source Code ; for mac

:: MORE INFORMATION

Citation

R.C. Edgar and E.W. Myers
PILER: identification and classification of genomic repeats.
Bioinformatics. 2005 Jun 1;21 Suppl 1:i152-i158

Evolver – Whole-genome Sequence Evolution Simulator

Evolver

:: DESCRIPTION

Evolver is a collection of programs designed to simulate the evolution of the nucleotide sequence of a whole genome. Evolver simulates the evolution of a representative genome of a species over periods long compared with its generation time.

::DEVELOPER

Robert Edgar , George Asimenos, Serafim Batzoglou and Arend Sidow.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Evolver

:: MORE INFORMATION

N/A

LikelyBin 0.1 – Metagenomic Binner

LikelyBin 0.1

:: DESCRIPTION

LikelyBin is an unsupervised metagenomic binner.

::DEVELOPER

WeitzGroup@GeorgiaTech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

LikelyBin ; Test data

:: MORE INFORMATION

Citation:

Andrey Kislyuk, Srijak Bhatnagar, Jonathan Dushoff and Joshua S. Weitz. Unsupervised Statistical Clustering of Environmental Shotgun Sequences. BMC Bioinformatics 2009, 10:316.