rSPR 1.3.0 – Calculate Rooted Subtree-prune-and-regraft Distances and rooted agreement forest

rSPR 1.3.0

:: DESCRIPTION

rSPR (rooted subtree-prune-and-regraft) is a software to calculate rooted subtree-prune-and-regraft distances and rooted agreement forests.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Perl
  • C++ Compiler

:: DOWNLOAD

  rSPR

:: MORE INFORMATION

Citation

Whidden, C., Beiko, R.G., Zeh, N.
Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments.
In: Proceedings of the 9th International Symposium on Experimental Algorithms, SEA 2010. Lecture Notes in Computer Science, vol. 6049, pp. 141–153. Springer-Verlag (2010)

PAUL 2.0 – Protein Distance Matrix Alignment

PAUL 2.0

:: DESCRIPTION

PAUL (Protein Alignment Using Lagrangian relaxation) is a tool for the computation of protein structure alignments based on sparse protein distance matrices

::DEVELOPER

Life Sciences Group, Centrum Wiskunde & Informatica

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • T-Coffee

:: DOWNLOAD

 PAUL

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2273-80. doi: 10.1093/bioinformatics/btq420. Epub 2010 Jul 17.
Towards optimal alignment of protein structure distance matrices.
Wohlers I1, Domingues FS, Klau GW.

FRETsg 1.0 – Structure Building from Multiple FRET Distances

FRETsg 1.0

:: DESCRIPTION

FRETsg is a tool for a fast qualitative analysis of multiple FRET (fluorescence resonance energy transfer) experiments. FRET experiments principally yield the distances between fluorescent dyes, which are commonly used for labelling proteins, DNA, RNA, etc. If multiple FRET experiments are done, it is possible to build a 3D model of the labelled positions. FRETsg finds all positions which obey the measured FRET distances and writes the model to a PDB-type file, which can be easily overlayed with other PDB structures.

::DEVELOPER

Gunnar Schröder and Helmut Grubmüller

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

 FRETsg

:: MORE INFORMATION

Citation

Schroeder, G., & Grubmueller, H. (2004).
FRETsg: Biomolecular structure model building from multiple FRET experiments.
Computer Physics Communications, 158(3), 150-157.

JaDis – Compute Distances between Nucleic Acid Sequences

JaDis

:: DESCRIPTION

JaDis is a program for computing distances between nucleic acid sequences. It allows specific comparison of coding sequences, of non-coding sequences, or of coding and non-coding sequences.

::DEVELOPER

 Atelier de BioInformatique

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsx/Linux
  • Java

:: DOWNLOAD

 JaDis

:: MORE INFORMATION

Citation

Goncalves I, Robinson M, Perriere G, Mouchiroud D.
JaDis: computing distances between nucleic acid sequences.
Bioinformatics. 1999 May;15(5):424-5.

MIDER v2 – Mutual Information Distance and Entropy Reduction

MIDER v2

:: DESCRIPTION

MIDER is a general purpose software tool for inferring network structures. It has been developed with biological networks in mind, but can be applied in other areas.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

MIDER

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • MatLab

:: DOWNLOAD

 MIDER

:: MORE INFORMATION

Citation

MIDER: Network Inference with Mutual Information Distance and Entropy Reduction.
Villaverde AF, Ross J, Morán F, Banga JR.
PLoS One. 2014 May 7;9(5):e96732. doi: 10.1371/journal.pone.0096732. eCollection 2014.

EMDomics 2.0.0 – Earth Mover’s Distance for Differential Analysis of Genomics Data

EMDomics 2.0.0

:: DESCRIPTION

The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups.

::DEVELOPER

Beck Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 EMDomics

:: MORE INFORMATION

Citation

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes.
Nabavi S, Schmolze D, Maitituoheti M, Malladi S, Beck AH.
Bioinformatics. 2015 Oct 29. pii: btv634.

DTscore – Fast and Accurate Distance Algorithm to Reconstruct Tandem Duplication Trees

DTscore

:: DESCRIPTION

DTscore is a distance based tamdem duplication tree reconstruction algorithm. It is based on a simple tandem duplication model, which assumes unequal recombination (crossover) as the only duplication mechanism. All it takes as input is a distance matrix between copies. In this matrix, the rows and columns need to be ordered in the same way as the copies are ordered on the locus. DTscore can be applied to relatively large datasets (more than a hundred copies). Distances can be calculated using programs such as DNADIST (nucleotide sequences) or PROTDIST (protein sequences) from the PHYLIP package. Heterogeneous rates of substitution among sites can be dealt with using the GAMMA method, for example.

::DEVELOPER

DTscore team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 DTscore

:: MORE INFORMATION

Citation

Elemento O. and Gascuel O.
An efficient and accurate distance based algorithm to reconstruct tandem duplication trees.
Bioinformatics. 2002 18 :S92-S99.

NucType 1.5 – Measure Distances/Size of Chromosomes and analysis Karyotype

NucType 1.5

:: DESCRIPTION

NucType is tool to measure distances/size of chromosomes, group the chromosomes and analysis the karyotype (karyotype asymmetry indices). Additionally it has a tool to measure the pollen or leaves.

::DEVELOPER

Yan Yu

:: SCREENSHOTS

NucType

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  NucType

:: MORE INFORMATION

MODICOS 2.4.1 – Morphometric and Distance Computation Software

MODICOS 2.4.1

:: DESCRIPTION

MODICOS allows to compute euclidean distances and centroid size (CS) from a set of coordinates x,y and use CS to estimate heritabilities and Qst. It also computes relative warps and uniform components of shape variation from a set of coordinates x,y and use any relative warp or uniform component to estimate heritabilities and Qst’s.

::DEVELOPER

Antonio Carvajal-Rodriguez 

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  MODICOS

:: MORE INFORMATION

Citation

Carvajal-Rodríguez A, Rodríguez MG 2005.
Morphometric and Distance Computation Software oriented for evolutionary studies.
Online Journal of Bioinformatics 6 : 34-41.

Hapstep 20010312 – Stepwise Analysis of Diversity for Haploid Data with Distance between Haplotypes

Hapstep 20010312

:: DESCRIPTION

Hapstep is based on the more simple program called HaPermut, except that analyses can be made in a stepwise manner, by combining related haplotypes progressively

::DEVELOPER

Rémy Petit (Petit@pierroton.inra.fr), INRA-Bordeaux

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 Hapstep

:: MORE INFORMATION

Citation

Pons O, Petit RJ.
Measuring and testing genetic differentiation with ordered versus unordered alleles.
Genetics 1996, 144:1237-1245