MPAlign-editor 3.0.0 – Graphical Tool for DNA and Protein Sequences and Alignments

MPAlign-editor 3.0.0

:: DESCRIPTION

MPAlign-editor is a graphical tool for DNA and Protein sequences and alignments.

::DEVELOPER

Frederico Arnoldi (fgcarnoldi@gmail.com)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Python

:: DOWNLOAD

 MPAlign-editor

:: MORE INFORMATION

Citation

MPAlign editor: uma ferramenta gráfica e intuitiva para alinhamentos moleculares.
Frederico GC Arnoldi 2005
Proceedings of II Workshop TIDIA—FAPESP

CotQuest 1.0 – Nonlinear Regression Analysis of DNA Reassociation Kinetics data

CotQuest 1.0

:: DESCRIPTION

CotQuest is specifically tailored to conduct nonlinear regression analysis of DNA reassociation kinetics (i.e., Cot) data when used with the statistics package SAS.  CotQuest is unique in that it does not require users to input guesses as to the final values of parameters.  The CotQuest program surpasses all existing Cot analysis programs with regard to automation, statistical robustness, user-friendliness, and graphical output.

:: DEVELOPER

the Institute for Genomics, Biocomputing & Biotechnology (IGBB).

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • SAS

:: DOWNLOAD

 CotQuest

:: MORE INFORMATION

Citation

Anal Biochem. 2009 May 15;388(2):322-30. doi: 10.1016/j.ab.2009.03.007.
CotQuest: improved algorithm and software for nonlinear regression analysis of DNA reassociation kinetics data.
Bunge J, Chouvarine P, Peterson DG.

WH – Fit Speciation Model to DNA Sequence data sets

WH

:: DESCRIPTION

WH is a computer program that carries out the fitting of a speciation model, and conducts tests of the quality of fit of that model.  The speciation model is called the Isolation Model, and is one without gene flow.  With comparative DNA sequence data from each of two closely related species, the method allows an estimation of the time since speciation and the size of the ancestral species.

::DEVELOPER

the Hey lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

  WH

:: MORE INFORMATION

R functions for cDNA array analysis – cDNA Microarray Analysis

R functions for cDNA array analysis

:: DESCRIPTION

R functions for cDNA array analysis is a set of R functions for filtering, normalization, Bayesian hierarchical modelling and MCMC procedures in cDNA microarray analysis.

::DEVELOPER

George C. Tseng 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  R functions for cDNA array analysis

:: MORE INFORMATION

Citation

George C. Tseng, Min-Kyu Oh, Lars Rohlin, James C. Liao, Wing Hung Wong (2001)
Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects,
Nucleic Acids Res v29 p2549

IDEAFIX – Refinement of Variants in FFPE DNA Sequencing data

IDEAFIX

:: DESCRIPTION

IDEAFIX is a decision tree-based variant refinement tool that filters formaldehyde-induced cytosine deaminations from variant lists obtained from DNA sequencing data from FFPE specimens.

::DEVELOPER

Maitena Tellaetxe Abete

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

IDEAFIX

:: MORE INFORMATION

Citation

Tellaetxe-Abete M, Calvo B, Lawrie C.
Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data.
NAR Genom Bioinform. 2021 Oct 27;3(4):lqab092. doi: 10.1093/nargab/lqab092. PMID: 34729472; PMCID: PMC8557387.

cutadapt v3.4 – Remove Adapter Sequences from DNA Sequencing reads

cutadapt v3.4

:: DESCRIPTION

Cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data.

::DEVELOPER

Marcel Martin @ the Science for Life Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 cutadapt

:: MORE INFORMATION

Citation

Marcel Martin
Cutadapt removes adapter sequences from high-throughput sequencing reads
EMBnet.journal volume 17 pages 10–12

TagGD – DNA Tag Generation and Demultiplexing

TagGD

:: DESCRIPTION

TagGD (DNA-based Tag Generator and Demultiplexor), a fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy.

::DEVELOPER

the Science for Life Laboratory, Uppsala University,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows

:: DOWNLOAD

  TagGD

:: MORE INFORMATION

Citation

PLoS One. 2013;8(3):e57521. doi: 10.1371/journal.pone.0057521. Epub 2013 Mar 4.
TagGD: fast and accurate software for DNA Tag generation and demultiplexing.
Costea PI, Lundeberg J, Akan P.

EuroForMix 3.3.3 – Statistical DNA Interpretation

EuroForMix 3.3.3

:: DESCRIPTION

EuroForMix is an advanced fully validated open-source, free software used to interpret complex DNA profiles (mixtures) taking into account peak height, stutter and degradation.

::DEVELOPER

EuroForMix team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

EuroForMix

:: MORE INFORMATION

Citation

Pascali VL.
A novel computational strategy to predict the value of the evidence in the SNP-based forensic mixtures.
PLoS One. 2021 Oct 15;16(10):e0247344. doi: 10.1371/journal.pone.0247344. PMID: 34653182; PMCID: PMC8519470.

DeepMP – Detect DNA modifications in Nanopore Sequencing data

DeepMP

:: DESCRIPTION

DeepMP is a convolutional neural network (CNN)-based model that takes information from Nanopore signals and basecalling errors to detect whether a read is methylated or not.

::DEVELOPER

DeepMP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • Python

:: DOWNLOAD

DeepMP

:: MORE INFORMATION

Citation:

Bonet J, Chen M, Dabad M, Heath S, Gonzalez-Perez A, Lopez-Bigas N, Lagergren J.
DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data.
Bioinformatics. 2021 Oct 28:btab745. doi: 10.1093/bioinformatics/btab745. Epub ahead of print. PMID: 34718417.

Exit mobile version