hap-ibd – Detect Identity-by-descent Segments

hap-ibd

:: DESCRIPTION

The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data.

::DEVELOPER

Brian L. Browning

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

hap-ibd

:: MORE INFORMATION

Citation:

Zhou Y, Browning SR, Browning BL.
A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data.
Am J Hum Genet. 2020 Apr 2;106(4):426-437. doi: 10.1016/j.ajhg.2020.02.010. Epub 2020 Mar 12. PMID: 32169169; PMCID: PMC7118582.

Pafig 1.0 – Prediction of Amyloid Fibril-forming Segments

Pafig 1.0

:: DESCRIPTION

Pafig based on support vector machines, exploited 41 physicochemical properties to identify the specific regions associated with fibrillar aggregates.

::DEVELOPER

Biotechnology Research Institute, Chinese Academy of Agricultural Sciences

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Windows
Perl

:: DOWNLOAD

Pafig

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S45. doi: 10.1186/1471-2105-10-S1-S45.
Prediction of amyloid fibril-forming segments based on a support vector machine.
Tian J1, Wu N, Guo J, Fan Y.

LHiSA 20080507 – Local High-scoring Segments for Association

LHiSA 20080507

:: DESCRIPTION

LHiSA is an algorithm dedicated to large-scale association studies which aims to identify segments of genome involved in a disease. It is based on Local Score statistic and an automatic selection of the significant segments.

::DEVELOPER

SSB group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/MacOsX
C++ Compiler / R package

:: DOWNLOAD

LHiSA

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2006;5:Article22. Epub 2006 Sep 17.
Detecting local high-scoring segments: a first-stage approach for genome-wide association studies.
Guedj M, Robelin D, Hoebeke M, Lamarine M, Wojcik J, Nuel G.

seg-suite – Manipulate Segments and Alignments

seg-suite

:: DESCRIPTION

The seg suite provides tools for manipulating segments and alignments.

::DEVELOPER

Martin Frith

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ compiler

:: DOWNLOAD

seg-suite

:: MORE INFORMATION

Segway 3.0.3 – a way to Segment the Genome

Segway 3.0.3

:: DESCRIPTION

Segway contains a novel method for analyzing multiple tracks of functional genomics data. Our method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling.

::DEVELOPER

Noble Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
python

:: DOWNLOAD

Segway

:: MORE INFORMATION

Citation

Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes J, Noble WS. 2012.
Unsupervised pattern discovery in human chromatin structure through genomic segmentation.
Nat Methods. 2012 Mar 18;9(5):473-6. doi: 10.1038/nmeth.1937.

Segment 1.04 – Identifying Compositional Domains in DNA Sequences

Segment 1.04

:: DESCRIPTION

Segment is a heuristic segmentation algorithm for DNA sequences. The program divides a DNA sequence into compositionally homogeneous domains by iterating a local optimization procedure at a given statistical significance.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Segment

:: MORE INFORMATION

Citation:

Oliver JL, Román-Roldán R, Pérez J, Bernaola-Galván P. 1999.
SEGMENT: identifying compositional domains in DNA sequences.
Bioinformatics 15: 974-979

HapFABIA 1.28.0 – Identification of very short Segments of IBD Characterized by Rare Variants

HapFABIA 1.28.0

:: DESCRIPTION

HapFABIA (Factor Analysis for Bicluster Acquisition) is an R package for identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux / MacOsX
R
BioConductor

:: DOWNLOAD

HapFABIA

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Dec;41(22):e202. doi: 10.1093/nar/gkt1013. Epub 2013 Oct 29.
HapFABIA: identification of very short segments of identity by descent characterized by rare variants in large sequencing data.
Hochreiter S

CMEIAS Color Segmentation 1.0 – Segment & Analyze Foreground Objects within Complex Images

CMEIAS Color Segmentation 1.0

:: DESCRIPTION

CMEIAS Color Segmentation is a free, improved computing technology designed to alleviate the laborious task of segmenting foreground objects of interest (e.g., microbes) from background in complex digital micrographs, as commonly encountered when preparing digital images of microbial populations and communities in environmental samples for quantitative image analysis.

::DEVELOPER

CMEIAS Team

:: SCREENSHOTS