:: DESCRIPTION
UniDPlot is designed to easily search for short sequences in large genomic contig.
::DEVELOPER
Marc Girondot & Jean-Yves Sire
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Girondot, M. and J.-Y. Sire 2010.
UniDPlot : A software to detect weak similarities between two DNA sequences.
Journal of Bioinformatics and Sequence Analysis 2(5): 69-74.
:: DESCRIPTION
Siscan is a C program for detecting recombination in a set of aligned DNA or amino acid sequences.
::DEVELOPER
SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Hybsweeper was developed to handle images of high-density gridding patterns which were matched to clones housed in microtiter dishes. As high-throughput methodologies contribute to large archives of stored clone resources, methods need to be available for convenient processing of hybridization information for the retrieval of the clones needed for research endeavors. A Java software package, Hybsweeper, was developed to select clone identities from autoradiographs which were generated through simple probing methods, overgo probe hybridizations, and isolation of unique clones from saturation hybridization.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gerard R. Lazo, Nancy Lui, Yong Q. Gu, Xiuying Kong, Devin Coleman-Derr, and Olin D. Anderson.
Hybsweeper: a resource for detecting high-density plate gridding coordinates
BioTechniques (2005) 39:320-324.
:: DESCRIPTION
The LnLCorr package is designed to detect pairwise coevolutionary among residues in a set of proteins using likelihood ratio tests.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wang ZO, Pollock DD:
Coevolutionary patterns in cytochrome coxidase subunit I depend on structural and functional context.
J Mol Evol 2007, 65(5):485-495
:: DESCRIPTION
SplazerS (Split Read Mapping as a branch of RazerS) is a tool for mapping reads containing structural variants, implemented in the highly efficient SeqAn C++ software library. SplazerS employs “split” read mapping, where prefix and suffix match of a read may be interrupted by a longer gap. This split read mapping is useful in the context of mRNA sequencing, where introns cause so-called junction reads that span exon-exon boundaries, or for the detection of small to medium-sized insertions and deletions in genomic data.
::DEVELOPER
Anne-Katrin Emde, David Weese, Marcel Schulz, Stefan Haas, and Knut Reinert
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Anne-Katrin Emde et al.
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS
Bioinformatics (2012) 28 (5): 619-627.
:: DESCRIPTION
biomc2 is a hierarchical Bayesian procedure to detect recombination in DNA sequence alignments based on the incongruence between topologies caused by recombinational events.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Leonardo de Oliveira Martins, élcio Leal and Hirohisa Kishino (2008)
Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees.
PLoS ONE 3(7): e2651.
:: DESCRIPTION
MLOGD (Maximum Likelihood Overlapping Gene Detector) is a suite of software for detecting new protein-coding sequences (CDSs) by analysing the pattern of mutations across an input sequence alignment. In particular, the software can be used to detect new CDSs that overlap known CDSs in a different read-frame. Such CDSs can be difficult to detect with standard gene-finding algorithms (see below). The software is particularly useful for analysing virus genome alignments, where overlapping genes and ribosomal frameshifting sites are common.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Firth A. E., Brown C. M., 2006,
Detecting Overlapping Coding Sequences in Virus Genomes,
BMC Bioinformatics, 7, 75.
:: DESCRIPTION
LGT3State is a program for inferring lateral gene transfer (LGT) in cases where there are two non-homologous genes, where each gene performs the same function (which is essential to the cell). Thus, there are three states which may characterize an organism: (a) it encodes gene A, (b) it encodes gene B, (c), it encodes both genes A and B.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Stern A., Mayrose I., Penn, O., Shaul S., Gophna U., Pupko T.
An Evolutionary Analysis of Lateral Gene Transfer in Thymidylate Synthase Enzymes.
Syst Biol. 2010 March; 59(2): 212–225.
:: DESCRIPTION
M-GCAT is a tool for rapidly visualizing and aligning the most highly conserved regions in multiple (typically prokaryote) genomes. M-GCAT is based upon a highly efficient approach to anchor-based multiple genome comparison using a compressed suffix graph and thus can construct multiple genome alignment frameworks in closely related species usually in a few minutes. A couple of important limitations include (1) input sequences MUST be assembled, and (2) the comparison is reference-sequence biased.
::DEVELOPER
the Algorithmics and Genetics Group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
T. Treangen and X. Messeguer.
M-GCAT: Interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species.
BMC Bioinformatics 2006, 7:433.
:: DESCRIPTION
CloseUp is a new algorithm for the statistical detection of chromosomal homology, which uses shared-gene density alone to fully exploit the observation that relaxing colinearity requirements in general is beneficial for homology detection and at the same time optimizes computation time. CloseUp has two components: the identification of candidate homologous regions followed by their statistical evaluation using Monte Carlo methods and data randomization.
::DEVELOPER
Institute for Genomics and Bioinformatics
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
S. Hampson, B.S. Gaut, and P. Baldi.
CloseUp: Statistical Detection of Chromosomal Homology Using Shared-Gene Density Alone.
Bioinformatics , 21, 8, 1339-1348, (2005).
