Tag: Reconstruction

Phyrex 1.1 – Reconstruction of Continuous Character Trait Values at nodes of Phylogenetic Trees

Phyrex 1.1

:: DESCRIPTION

Phyrex (PHYlogenetic REconstruction by use of gene eXpression and alternate mRNA splicing patterns) is a program for reconstructing ancestral gene expression profiles and sequence data on a given phylogenetic tree. The program uses a Minimum Evolution algorithm to reconstruct the gene expression profiles and a combination of BaseML and ClustalW to reconstruct the ancestral sequences.

::DEVELOPER

Roald Rossnes

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • C++ Compiler

:: DOWNLOAD

 Phyrex

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2005 May 27;6:127.
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.
Rossnes R, Eidhammer I, Liberles DA.

FT-COMAR – Fault Tolerance Reconstruction of 3D Structure from Protein Contact Maps

FT-COMAR

:: DESCRIPTION

FT-COMAR ( Fault Tolerant COntact MAp Reconstruction) implements a heuristic procedure for recovering a set of 3D coordinates from an incomplete contact map.

FT-COMAR Online Version

::DEVELOPER

 Bioinformatics group, Department of Computer Science, University of Bologna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

  FT-COMAR

:: MORE INFORMATION

Citation

FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps.
Vassura M, Margara L, Di Lena P, Medri F, Fariselli P, Casadio R.
Bioinformatics. 2008 May 15;24(10):1313-5. Epub 2008 Apr 1.

PFT3DR 20100707 – Compute 3D Reconstruction from 2D Projections of 3D Objects

PFT2/EM3DR2

:: DESCRIPTION

PFT3DR (PFT2/EM3DR2) is programs for computing three-dimensional reconstructions from two-dimensional projections of 3D objects.  The two programs were developed for three-dimensional electron microscopy–particularly biological macromolecules imaged by cryogenic electron microscopy.  PFT2 is used to determine orientations and origins of imaged particles.  EM3DR2 is used to compute three-dimensional reconstructions based on the orientation and origin parameters determined by PFT2 or other programs.

::DEVELOPER

David Belnap team (BYU, Provo, UT)

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • AIX/ Darwin (Mac OS X)/ IRIX (SGI)/Linux/Solaris/Tru64 (OSF1)/ OpenVMS
  • Bsoft

:: DOWNLOAD

PFT3DR

:: MORE INFORMATION

Citation for PFT2

Orientations and origins for windowed particles were determined via a modified version of the PFT algorithm (Baker and Cheng, 1996) altered to use both phase and amplitude information in orientation selection and to use non-icosahedral symmetries (Sanz-García et al., 2010).

Citation for EM3DR2

Three-dimensional reconstructions were computed with a Fourier-Bessel algorithm (Crowther et al., 1970; Fuller et al., 1996).

ANCESCON – ANCEStral sequence reCONstruction

ANCESCON

:: DESCRIPTION

ANCESCON is a package for distance-based phylogenetic inference and reconstruction of ancestral protein sequences that takes into account the observed variation of evolutionary rates between positions that more precisely describes the evolution of protein families.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ANCESCON

:: MORE INFORMATION

Citation:

W.Cai, J.Pei, and N.V.Grishin (2004)
“Reconstruction of ancestral protein sequences and its applications“.
BMC Evolutionary Biology 4(1): 33

Scripture Beta2 – Transcriptome Reconstruction

Scripture Beta2

:: DESCRIPTION

Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio.The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.

:DEVELOPER

Scripture Team

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 Scripture

:: MORE INFORMATION

Citation:

Mitchell Guttman et al.
Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
Nature Biotechnology 28, 503–510 (2010)

ALIFRITZ 1.0 – Statistical Multiple Alignment and Phylogeny Reconstruction

ALIFRITZ 1.0

:: DESCRIPTION

ALIFRITZ performs statistical multiple alignment and phylogeny reconstruction simultaneously. It  implements a strategy based on simulated annealing which makes use of these models to infer a phylogenetic tree for a set of DNA or protein sequences together with the sequences’ indel history, i.e. their multiple alignment augmented with information about the positioning of insertion and deletion events in the tree.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ALIFRITZ

:: MORE INFORMATION

Citation:

Roland Fleißner, Dirk Metzler and Arndt von Haeseler,
Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction.
Syst. Biol., 54, 548-561

ARACNE 2 – Reconstruction of Accurate Cellular Networks

ARACNE 2

:: DESCRIPTION

ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks), a novel algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis.

::DEVELOPER

the Califano lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ARACNE

:: MORE INFORMATION

Citation:

dam A Margolin et al.
ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Contex
BMC Bioinformatics. 2006; 7(Suppl 1): S7.

PolyPhy – Microbial Phylogeny Reconstruction with Polytomy Identification

PolyPhy

:: DESCRIPTION

PolyPhy (Polytomy Identification In Microbial Phylogeny) is a stand-alone phylogeny construction with polytomy identification tool. PolyPhy first constructes a microbial phylogeny with calculating a composite distance based on the comparison of complete gene sets between two genomes using ComPhy. And then it identifies bifurcating polytomies using Bayesian Logistic Regression classification from it.

::DEVELOPER

Digital Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 PolyPhy

:: MORE INFORMATION

Citation

Guan N Lin, Chao Zhang and Dong Xu
Polytomy identification in microbial phylogenetic reconstruction
BMC Systems Biology 2011, 5(Suppl 3):S2

Quicktree 1.1 – Reconstruction of Phylogenies for very large Protein Families

Quicktree 1.1

:: DESCRIPTION

QuickTree allows the reconstruction of phylogenies for very large protein families that would be infeasible using other popular methods.

::DEVELOPER

Kevin Howe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 Quicktree

:: MORE INFORMATION

Citation

QuickTree: building huge Neighbour-Joining trees of protein sequences.
Howe K, Bateman A and Durbin R
Bioinformatics 2002;18;11;1546-7

MaxAlike 1.0 – Phylogenetic Reconstruction of incomplete Sequences by Maximum Likelihood

MaxAlike 1.0

:: DESCRIPTION

MaxAlike algorithm aims at reconstructing a nucleotide sequence in a target species, based on a multiple sequence alignment and a phylogenetic tree of homologous sequences from other species. For each alignment position the probabilities of occurrence for each nucleotide are computed, considering the phylogenetic position of the target species in the tree.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MaxAlike

:: MORE INFORMATION

Citation:

P. Menzel, P. F. Stadler and J. Gorodkin:
maxAlike: Maximum-likelihood based sequence reconstruction with application to improved primer design for unknown sequences,
Bioinformatics, 2011, 27, 317-325.

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