UNAFold 4.0 / mfold 3.6 / MFold Interface 1.18 – Nucleic Acid Folding & Hybridization Package

UNAFold 4.0 / mfold 3.6 / MFold Interface 1.18

:: DESCRIPTION

UNAFold (Unified Nucleic Acid Folding & Hybridization Package) is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. Folding (secondary structure) prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling. For melting simulations, the package computes entire melting profiles, not just melting temperatures. UV absorbance at 260 nm, heat capacity change (C(p)), and mole fractions of different molecular species are computed as a function of temperature.

mfold has been replaced by UNAFold.Although UNAFold will install without mfold_util, the sir_graph and boxplot_ng programs from the mfold_util package are required in order to obtain structure plots and dot plots from UNAFold. Install mfold_util before installing UNAFold. Versions 3.4 and higher of mfold contains all of the non-interactive programs in mfold_util, so a separate download is not required.

MFold Interface is Perl/Tk GUI Interface for Dr. Michael Zuker’s MFold.

::DEVELOPER

UNAFold team

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / Mac OsX
glut/OpenGL
GD Library
gnuplot
perl

:: DOWNLOAD

UNAFold ; mfold , MFold Interface

:: MORE INFORMATION

Citation

Methods Mol Biol. 2008;453:3-31.
UNAFold: software for nucleic acid folding and hybridization.
Markham NR, Zuker M.

FISHtrees 3.2.0 – Phylogenetic Analysis of Multiprobe Fluorescence in situ Hybridization data

FISHtrees 3.2.0

:: DESCRIPTION

“FISHtrees” is a software program:
1) to parse copy numbers of multiple Fluorescence In Situ Hybridization (FISH) probe signals in a single-cell assay;
2) to analyze probe signals across multiple single-cell assays in a patient data file;
3) to model tumorigenesis as a tree of tumor progression paths for a given probe on a given patient data file;
4) to merge multiple tumorigenesis trees to represent multiple probes on a given patient data file;
5) to compute consensus multiple joint tumorigenesis trees representing multiple patient data files into a network as a graph of tumor progression pathways.

::DEVELOPER

FISHtrees team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

FISHtrees

:: MORE INFORMATION

Citation

Gertz EM, et al.
FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe.
PLoS One. 2016 Jun 30;11(6):e0158569. doi: 10.1371/journal.pone.0158569. PMID: 27362268; PMCID: PMC4928784.

Bioinformatics. 2013 Jul 1;29(13):i189-98. doi: 10.1093/bioinformatics/btt205.
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations.
Chowdhury SA1, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R.

HyDe v0.4.3 – Hybridization Detection

HyDe v0.4.3

:: DESCRIPTION

HyDe is a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization.

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Python

:: DOWNLOAD

HyDe

:: MORE INFORMATION

Citation

HyDe: A Python Package for Genome-Scale Hybridization Detection.
Blischak PD, Chifman J, Wolfe AD, Kubatko LS.
Syst Biol. 2018 Sep 1;67(5):821-829. doi: 10.1093/sysbio/syy023.

STEM 2.0 / STEM-hy 1.0 – Species Tree Estimation using Maximum likelihood (with hybridization)

STEM 2.0 / STEM-hy 1.0

:: DESCRIPTION

STEM-hy is a program for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Java

:: DOWNLOAD

STEM / STEM-hy

:: MORE INFORMATION

Citation

Kubatko, L., B. C. Carstens, and L. L. Knowles. 2009.
STEM: Species Tree Estimation using Maximum likelihood for gene trees under coalescence,
Bioinformatics (2009) 25 (7): 971-973.doi: 10.1093/bioinformatics/btp079

TS4MSBH – Tabu search algorithm for DNA Sequencing by Hybridization problem

TS4MSBH

:: DESCRIPTION

TS4MSBH is a tabu search algorithm for DNA sequencing by hybridization problem with a partial multiplicity information (a test set included)

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
.NET Framework 3.5

:: DOWNLOAD

TS4MSBH

:: MORE INFORMATION

Tabusearch – DNA Sequencing by Hybridization with Isothermic Libraries

Tabusearch

:: DESCRIPTION

Tabusearch is a sofrware for DNA sequencing by hybridization with isothermic libraries.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

Tabusearch

:: MORE INFORMATION

Citation

J. Blazewicz, P. Formanowicz, M. Kasprzak, W.T. Markiewicz, A. Swiercz,
“Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries“,
Computational Biology and Chemistry 28, 2004, pp. 11-19.

OligoWalk 2 – Select Efficient siRNA using Hybridization Thermodynamics

OligoWalk 2

:: DESCRIPTION

OligoWalk is an online sever calculating thermodynamic features of sense-antisense hybidization. It predicts the free energy changes of oligonucleotides binding to a target RNA. It can be used to design efficient siRNA targeting a given mRNA sequence.

::DEVELOPER

Mathews group

:: REQUIREMENTS

Linux

:: DOWNLOAD

OligoWalk

:: MORE INFORMATION

Citation:

Efficient siRNA selection using hybridization thermodynamics
Zhi John Lu and David H. Mathews
Nucl. Acids Res. (2008) 36 (2): 640-647