GACT – Genome Build and Allele Definition Conversion Tool

GACT

:: DESCRIPTION

GACT predicts and inter-converts between any of the common SNP allele definitions and between the major genome builds.

::DEVELOPER

Li Laboratory of Human Genetics and Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GACT

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jul 19;15:610. doi: 10.1186/1471-2164-15-610.
GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies.
Sulovari A, Li D

SuperTree 0.85b – Build Phylogenetic Supertrees

SuperTree 0.85b

:: DESCRIPTION

SuperTree is a software to build phylogenetic supertrees. It implements the MRP algorithm to assemble source trees into a supertree.

::DEVELOPER

Computational Phylogenetics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java

:: DOWNLOAD

SuperTree

:: MORE INFORMATION

Citation

N. Salamin, T.R. Hodkinson and V. Savolainen (2002).
Building supertrees: an empirical assessment using the grass family (Poaceae).
Syst. Biol. 51(1): 136-150

BMapBuilder 3.1 – Build Chromosome-wide LD Maps

BMapBuilder 3.1

:: DESCRIPTION

BMapBuilder builds maps of pairwise linkage disequilibrium (LD) in either two or three dimensions. The optimized resolution allows for graphical display of LD for single nucleotide polymorphisms (SNPs) in a whole chromosome.

::DEVELOPER

Bios, University of GranadaGranada , Spain

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BMapBuilder

:: MORE INFORMATION

Citation:

Abad-Grau, M.M.; Montes, R.; Sebastiani, P.
Building chromosome-wide LD maps“,
Bioinformatics 22(16): 1933-1934 (2006)

FPC 9.4 – Build Contigs from Fingerprinted Clones

FPC 9.4

:: DESCRIPTION

FPC (fingerprinted contigs)is an interactive program for building contigs from fingerprinted clones, where the fingerprint for a clone is a set of restriction fragments.FPC has an algorithm to automatically cluster clones into contigs based on their probability of coincidence score. For each contig, it builds a consensus band (CB) map which is similar to a restriction map but it does not try to resolve all the errors. The CB map is used to assign coordinates to the clones based on their alignment to the map and to provide a detailed visualization of the clone overlap. FPC has editing facilities for the user to refine the coordinates and to remove poorly fingerprinted clones. Functions are available for updating an FPC database with new clones. Contigs can easily be merged, split or deleted. Markers can be added to clones and are displayed with the appropriate contig. Sequence ready clones can be selected and their sequencing status displayed. As such, FPC is an integrated program for the assembly of sequence ready clones for large scale sequencing projects

:: DEVELOPER

Arizona Genomics Computational Lab (AGCoL)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 FPC

:: MORE INFORMATION

Citation:

Nelson, W. and C. Soderlund (2009).
Integrating Sequence with FPC Fingerprinted Maps.
Nucleic Acids Research 1-11 doi:10.1093/nar/gkp034

CellExplorer 1.0 – 3D C. elegans atlas Building & Application Tools

CellExplorer 1.0

:: DESCRIPTION

CellExplorer is a package of computer programs to process and analyze 3D confocal image stacks of the model animal C. elegans, and can be applied to several other model systems such as fruit fly embryo/larvae as well. Some other applications include 3D cell/nuclei segmentation, quantification, gene expression analysis, automatic cell naming/annotation, cell targeting, etc.

::DEVELOPER

Peng Lab @ JANELIA of HHMI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

CellExplorer

:: MORE INFORMATION

Citation:

Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart Kim, and Eugene Myers,
A 3D digital atlas of C. elegans and its application to single-cell analyses,”
Nature Methods, doi:10.1038/nmeth.1366, 2009.