SEMPHY 2.0 b3 – Structural EM Phylogenetic Reconstruction

SEMPHY 2.0 b3

:: DESCRIPTION

SEMPHY is a tool for data-intensive phylogenetic reconstruction. SEMPHY infers phylogenies by Maximum Likelihood, the most established criterion for finding the correct phylogenetic tree.

::DEVELOPER

Nir Friedman’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/ MacOsX

:: DOWNLOAD

SEMPHY

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Jan 15;23(2):e136-41.
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates.
Ninio M, Privman E, Pupko T, Friedman N.

EM – Estimate Genetic Distances and Chiasma Distribution for Human UPD and Trisomy data

EM

:: DESCRIPTION

EM is a software to estimate genetic distances and chiasma distribution for human UPD and trisomy data.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

:: MORE INFORMATION

Citation

Am J Hum Genet. 2001 Dec;69(6):1255-65. Epub 2001 Nov 5.
Multipoint genetic mapping with trisomy data.
Li J, Sherman SL, Lamb N, Zhao H.

SpaCEM3 2.0 – Spatial Clustering with EM and Markov Model

SpaCEM³ 2.0

:: DESCRIPTION

The SpaCEM³ software is dedicated to Spatial Clustering with EM and Markov Models. It proposes a variety of algorithms for supervised and unsupervised classification of multidimensional and spatially-located data. The main techniques use the EM algorithm for soft clustering and Markov Random Fields (MRF) for spatial modelling. The learning and inference parts are based on recent developments in mean field-like approximations. Its applications range from image segmentation (e.g. tissue detection in MRI, retrieval of planet surface properties from hyperspectral satellite images…) to gene clustering (e.g. biological module detection), remote sensing and mapping epidemics of ecological species.

::DEVELOPER

SpaCEM³ Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux

:: DOWNLOAD

SpaCEM³

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Mar 15;27(6):881-2. doi: 10.1093/bioinformatics/btr034. Epub 2011 Feb 3.
SpaCEM3: a software for biological module detection when data is incomplete, high dimensional and dependent.
Vignes M, Blanchet J, Leroux D, Forbes F.

tripleM 1.0 – Use Partition-Ligation strategy and EM Algorithm to Reconstruct Hplotypes in trios

tripleM 1.0

:: DESCRIPTION

tripleM is extended from the PL-EM program (Qin et al. 2002). It is for haplotype reconstruction when parental genotype information is available . Genotypes from all three members of the trios are assumed known. the format of the input file is the same as in PL-EM.

::DEVELOPER

Steve Qin @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows

:: DOWNLOAD

tripleM

:: MORE INFORMATION

Contact: questions, comments and suggestions are greatly appreciated, and can be sent to Steve Qin, qin@umich.edu, (734)-763-5965.

Maptools 1.0 – Deal with Experimental (X-ray, EM) 3D Maps

Maptools 1.0

:: DESCRIPTION

Maptools is a small collection of programs for working with experimental three-dimensional (density) maps.The programs are:

pdb2map Create a map from a coordinate file.
pdb2mask Create a mask from a coordinate file.
mapstat Calculate map statistics around a molecular fragment.
rottrans Perform a rigid body search for the best orientation of a structural fragment in a map.
extract Create coordinate files from rottrans output.
display Generate a pseuso-density map from rottrans output.

::DEVELOPER

Bert de Groot

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Maptools

:: MORE INFORMATION

Please send your bug reports, comments and suggestions to: bgroot@gwdg.de.