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).
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.
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.
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.
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.
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.
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 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