SimPlot 3.5.1 – Sequence Similarity Plotting

SimPlot 3.5.1

:: DESCRIPTION

SimPlot (Similarity Plotting) (as well as bootscanning, quick tree generation, and informative-sites analysis) is a popular tool for recombination analysis.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SimPlot if you cannot make that work, please email me for a download link

:: MORE INFORMATION

Reference to the paper in which author first described SimPlot

Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC.
Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.
J Virol. 1999 Jan;73(1):152-60.

VisSPA 1.62 – Calculate Frequency of Residues

VisSPA 1.62

:: DESCRIPTION

VisSPA (Visual Signature Pattern Analysis) is a program that accepts an alignment of sequences, interactively analyzes frequencies of residues at each position in groups of sequences and supports the generation of sequence logos. The frequency calculations and program name were initially inspired by VESPA (by Gerry Myers and Bette Korber of Los Alamos National Labs).

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

VisSPA

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

VarPlot 1.2 – Similarity Plotting for Alignment of Sequences

VarPlot 1.2

:: DESCRIPTION

VarPlot is a program that accepts an alignment of sequences, and interactively plots sliding-window analyses of genetic distance among sequences or groups of sequences. It is different from SimPlot because in SimPlot, all groups are compared to one query, whereas in VarPlot all groups are compared to one another. Also, VarPlot includes calculation of nonsynonymous and synonymous distance (using the Nei and Gojobori method at present).

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

VarPlot

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

MargFreq 1.02 – Calculate Marginal Frequencies at each Position of a Nucleotide/Amino Acid Sequence

MargFreq 1.02

:: DESCRIPTION

MargFreq is a relatively user-friendly Windows program that does a repetitive task – calculating the marginal frequencies at each position of a nucleotide/amino acid sequence. This program accepts sequence alignments in many different formats. It also does some rudimentary analysis for covariation.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MargFreq

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

CleanCollapse 1.0.5 – Transfer Alignment of Sequences into Single Sequence

CleanCollapse 1.0.5

:: DESCRIPTION

CleanCollapse is a relatively user-friendly Windows program that accepts an alignment of sequences, and optionally can remove rare sporadic polymorphisms that may represent analytical artifacts, and also reduce redundancy by “collapsing” identical sequences into a single sequence. The program provides a record of these manipulation, and some rudimentary analysis (e.g. proportion of synonymous and nonsynonymous sporadic changes) that may assist interpretation

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

CleanCollapse

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

NimbleTree 2.6 – Make Phylogenetic Trees from Sequence Data

NimbleTree 2.6

:: DESCRIPTION

NimbleTree is a relatively user-friendly Windows program for making phylogenetic trees starting from sequence data.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

NimbleTree

:: MORE INFORMATION

Before you download software you need to read disclaimer.

ReadDepth 0.9.8.4 – Detects Copy Number Aberrations in Deep Sequencing Data

ReadDepth 0.9.8.4

:: DESCRIPTION

The readDepth package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. It achieves higher accuracy than many other packages, and runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets.

::DEVELOPER

the Bioinformatics Research Laboratory at Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package

:: DOWNLOAD

 ReadDepth

:: MORE INFORMATION

Citation

Miller CA, Hampton O, Coarfa C, Milosavljevic A, 2011
ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads.
PLoS ONE 6(1): e16327. doi:10.1371/journal.pone.0016327

LSR – Estimate Region-specific p-values in Genetic Association Mapping studies

LSR

:: DESCRIPTION

LSR (Longest Run Test) is an S-plus program computes the distribution and the first moment of the length of the longest k-interrupted run (Lk) in a binary sequence.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • S-plus

:: DOWNLOAD

  LSR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 May 27;9:246. doi: 10.1186/1471-2105-9-246.
Using the longest significance run to estimate region-specific p-values in genetic association mapping studies.
Lian IeB, Lin YH, Lin YC, Yang HC, Chang CJ, Fann CS.

CNIT 5.1 – Copy Number Inferring tool

CNIT 5.1

:: DESCRIPTION

CNIT is designed for Affymetrix GeneChip to analyze copy number of each SNP allele. CNIT can be applicable in chromosome-abnormal disease, cancer and copy number variation studies, and can provide accurate CN estimations with low false-positive rate.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R package

:: DOWNLOAD

 CNIT

:: MORE INFORMATION

Citation

Genome-wide copy number analysis using copy number inferring tool (CNIT) and DNA pooling.
Lin CH, Huang MC, Li LH, Wu JY, Chen YT, Fann CS.
Hum Mutat. 2008 Aug;29(8):1055-62

HIERFSTAT 0.5-10 – Package for R to Compute & Test Hierarchical F-statistics

HIERFSTAT 0.5-10

:: DESCRIPTION

HIERFSTAT is a package for R allowing to estimate F-statistics and variance components with the methods of moments for any number of levels in a hierarchy. The package also allows to test the significance of population differentiation using the likelihood ratio G-statistic or the variance components.

::DEVELOPER

Jérôme Goudet.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HIERFSTAT

:: MORE INFORMATION

Citation

Goudet, J. (2005)
Hierfstat, a package for R to compute and test hierarchical F-statistics.
Molecular Ecology Notes. 5: 184-186