REAGO 1.1 – REconstruct 16S ribosomal RNA Genes from MetagenOmic data

REAGO 1.1

:: DESCRIPTION

REAGO is an assembly tool for 16S ribosomal RNA recovery from metagenomic data

::DEVELOPER

Cheng Yuan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 REAGO

:: MORE INFORMATION

Citation

Reconstructing 16S rRNA genes in metagenomic data.
Yuan C, Lei J, Cole J, Sun Y.
Bioinformatics. 2015 Jun 15;31(12):i35-i43. doi: 10.1093/bioinformatics/btv231.

BiRW – Reconstruct Disease Phenome-genome Association

BiRW

:: DESCRIPTION

BiRW (Bi-Random Walk)is an algorithm to capture the CBG patterns in the networks for unveiling the associations between the complete collection of disease phenotypes (phenome) and genes.

::DEVELOPER

Rui Kuang 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Matlab

:: DOWNLOAD

 BiRW

:: MORE INFORMATION

Citation

MaoQiang Xie, TaeHyun Hwang and Rui Kuang
Reconstructing Disease Phenome-genome Association by Bi-Random Walk
Bioinformatics (2012)doi: 10.1093/bioinformatics/bts06

BitPhylogeny 0.99 – Reconstruct Intra-tumor Evolutionary Pathways

BitPhylogeny 0.99

:: DESCRIPTION

BitPhylogeny is a probabilistic framework to reconstruct intra-tumor evolutionary pathways.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • R

:: DOWNLOAD

 BitPhylogeny

:: MORE INFORMATION

Citation

Genome Biol. 2015 Feb 13;16:36. doi: 10.1186/s13059-015-0592-6.
BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.
Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N.

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.

RASP 3.2 – Reconstruct Ancestral State in Phylogenies

RASP 3.2

:: DESCRIPTION

RASP is a tool for inferring ancestral state using S-DIVA (Statistical dispersal-vicariance analysis), Lagrange (DEC), Bayes-Lagrange (S-DEC), BayArea, BBM (Bayesian Binary MCMC), BayesTraits and ChromEvol.

::DEVELOPER

Yan Yu

:: SCREENSHOTS

RASP

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

  RASP

 :: MORE INFORMATION

Citation

S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring biogeographic histories.
Yu Y, Harris AJ, He X.
Mol Phylogenet Evol. 2010 Aug;56(2):848-50. doi: 10.1016/j.ympev.2010.04.011

RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography.
Yu Y, Harris AJ, Blair C, He X.
Mol Phylogenet Evol. 2015 Mar 26;87:46-49. doi: 10.1016/j.ympev.2015.03.008.

Reconstruct 1.0 – Reconstructing 3D Structures from Contact Maps

Reconstruct 1.0

:: DESCRIPTION

RECONSTRUCT is a command line program for reconstruction of protein contact maps that uses the distgeom program of the TINKER package.

::DEVELOPER

the Bioinformatics / Structural Proteomics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Tinker

:: DOWNLOAD

 Reconstruct

:: MORE INFORMATION

Citation

Optimal contact definition for reconstruction of Contact Maps.
Jose M Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis and Michael Lappe.
BMC Bioinformatics 2010, 11:283.

vPhyloMM 20090731 – Reconstructs Mutational Pathways of Drug Resistance

vPhyloMM 20090731

:: DESCRIPTION

The purpose of vPhyloMM is to generate a transition model showing the mutational pathways of drug resistance for viruses under drug pressure.

::DEVELOPER

Bioinformatics Research Group (BioRG)

:: SCREENSHOTS

vPhyloMM

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl
  • Active Perl 

:: DOWNLOAD

 vPhyloMM

:: MORE INFORMATION

Citation:

Buendia, P., Cadwallader, B. and DeGruttola, V. (2009)
A phylogenetic and Markov model approach for the reconstruction of mutational pathways of drug resistance.
Bioinformatics. 2009 Oct 1;25(19):2522-9. doi: 10.1093/bioinformatics/btp466.

PhyloQuart 1.4 – Reconstruct Phylogenies from Quartets

PhyloQuart 1.4

:: DESCRIPTION

PhyloQuart is a collection of programs aimed at estimating phylogenies from a quartet principle.

::DEVELOPER

Vincent Berry, and David Bryant

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 PhyloQuart

:: MORE INFORMATION

Citation

Vincent Berry, and David Bryant
Faster reliable phylogenetic analysis.
RECOMB (1999) , p. 59-68.

 

PhyNav 1.0 – Reconstruct Evolutionary Relationship among Contemporary Species based on Genetic data

PhyNav 1.0

:: DESCRIPTION

PhyNav (Phylogenetic Navigator)is a tree sampling method to reconstruct phylogenetic trees from really large datasets (DNA and protein). The method combines different methods to sample good trees.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PhyNav

:: MORE INFORMATION

Citation:

Le Sy Vinh, Heiko A. Schmidt and Arndt von Haeseler,
PhyNav: A novel approach to reconstruct large phylogenies,
proceedings of GfKl conference, 2004.

IQPNNI 3.3.2 – Reconstruct a Phylogenetic Tree based on DNA or Amino Acid Sequence data

IQPNNI 3.3.2

:: DESCRIPTION

IQPNNI (Important Quartet Puzzling and NNI Operation) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast algorithms to generate a list of potential candidate trees. The key ingredient is the definition of so-called important quartets (IQs), which allow the computation of an intermediate tree in O(n^2) time for n sequences. The resulting tree is then further optimized by applying the nearest neighbor interchange (NNI) operation. Subsequently a random fraction of the sequences is deleted from the best tree found so far. The deleted sequences are then re-inserted in the smaller tree using the important quartet puzzling (IQP) algorithm.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

  IQPNNI

:: MORE INFORMATION

Citation:

Le Sy Vinh and Arndt von Haeseler (2004)
IQPNNI: Moving fast through tree space and stopping in time.
Mol. Biol. Evol., 21(8):1565-1571.