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.

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.

 

FaBox 1.61 – Online FASTA Sequences Toolbox

FaBox 1.61

:: DESCRIPTION

FaBox is a collection of simple and intuitive web services that enable biologists and medical researchers to quickly perform typical task with sequence data. The services makes it easy to extract, edit, and replace sequence headers and join or divide data sets based on header information. Other services include collapsing a set of sequences into haplotypes and automated formatting of input files for a number of population genetics programs, such as ARLEQUIN , TCS and MRBAYES . The toolbox is expected to grow on the basis of requests for particular services and converters in the future.

::DEVELOPER

Palle Villesen Fredsted

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • WebServer
  • PHP

:: DOWNLOAD

 FaBox

:: MORE INFORMATION

Citation

Villesen, P (2007),
FaBox: an online toolbox for fasta sequences,
Molecular Ecology Notes 7 (6), 965-968. doi:10.1111/j.1471-8286.2007.01821.x

GP 0.26 / Arka 0.11 – Sequence Manipulation tools

GP 0.26 / Arka 0.11

:: DESCRIPTION

GP and Arka are very leightweighed programs for manipulation of DNA / RNA / protein sequences. They are designed on one hand to run smoothly on older machines, and on the other — to faciliate processing of large numbers of sequence / data files. GP includes utilities to convert DNA / RNA to protein, determine codon usage / GC contents, promotor searches, Tm, searching for restriction sites, converting sequences into numerical representations and much more.

::DEVELOPER

Dr. January Weiner 3rd

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GP  / Arka

:: MORE INFORMATION

WH – Fit Speciation Model to DNA Sequence data sets

WH

:: DESCRIPTION

WH is a computer program that carries out the fitting of a speciation model, and conducts tests of the quality of fit of that model.  The speciation model is called the Isolation Model, and is one without gene flow.  With comparative DNA sequence data from each of two closely related species, the method allows an estimation of the time since speciation and the size of the ancestral species.

::DEVELOPER

the Hey lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

  WH

:: MORE INFORMATION

R’MES 3.1.0 – Finding Exceptional Motifs in Sequences

R’MES 3.1.0

:: DESCRIPTION

R’MES is a set of C++ programs devoted to the detection of motifs with an exceptional frequency in sequences (DNA, protein or other).The main question R’MES addresses is “does this motif occur in that biological sequence with an expected frequency?” In other words, can we observe it so many times, or so few times, just by chance? Usually, when the answer is no, such a motif is a candidate to have a particular biological meaning; only a candidate: statistical significance is not equivalent to biological significance.

::DEVELOPER

SSB group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

:: MORE INFORMATION

Citation

Schbath, S. and Hoebeke, M. (2011).
R’MES: a tool to find motifs with a significantly unexpected frequency in biological sequences.
In Advances in genomic sequence analysis and pattern discovery (L. Elnitski, O. Piontkivska, and L. Welch, eds.). Science, Engineering, and Biology Informatics, vol. 7. World Scientific.

GeneViewer v.1 – View Genes and Features along a Sequences

GeneViewer v.1

:: DESCRIPTION

GeneViewer is very simple program for visualising the locations of various genomic features (SNPs, exons etc.)along a sequence. The user enters start and stop coordinates of the region they’re interested in, followed by any number of files. Each file must contain 2 columns of data (region start & stop) with any number of rows

::DEVELOPER

Colm O’Dushlaine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows
  • Perl

:: DOWNLOAD

 GeneViewer

:: MORE INFORMATION

Refget v0.1.0 – Refget Sequence Identification and Retrieval

Refget v0.1.0

:: DESCRIPTION

Refge is a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from the sequence itself.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Refget

:: MORE INFORMATION

Citation

Yates AD, Adams J, Chaturvedi S, Davies RM, Laird M, Leinonen R, Nag R, Sheffield NC, Hofmann O, Keane TM.
Refget: standardised access to reference sequences.
Bioinformatics. 2021 Jul 14:btab524. doi: 10.1093/bioinformatics/btab524. Epub ahead of print. PMID: 34260694.

MetaCherchant – Analysing Genomic Environment of a Nucleotide Sequence within a Metagenome

MetaCherchant

:: DESCRIPTION

MetaCherchant is a tool for analyzing genomic context of antibiotic resistance genes in gut microbiota.

::DEVELOPER

Computer Technologies Laboratory, National Research University of Information Technologies,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOs
  • JRE
:: DOWNLOAD

MetaCherchant

:: MORE INFORMATION

Citation

Olekhnovich EI, Vasilyev AT, Ulyantsev VI, Kostryukova ES, Tyakht AV.
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota.
Bioinformatics. 2018 Feb 1;34(3):434-444. doi: 10.1093/bioinformatics/btx681. PMID: 29092015.