Sequences

Recco analyzes alignments of sequences that evolved subject to recombination and mutation. The analysis provides evidence as to whether a dataset contains recombination, which sequence is a recombinant and where the recombination breakpoints are. The analysis is based on explaining one sequence...

miRpp - A Plant microRNA Precursor Prediction Tool for Small RNA Reads on Genome Sequences

JDSA is a Java program that will degenerately search DNA sequences. This program searches sequences for multiple nucleotides at a given position (positional degeneracy), limited overall sequence accuracy (group degeneracy) or variable spacing between multiple DNA sequences (spacing degeneracy)....


Platforms: Mac

ProteinMusic is a Java program converting DNA sequences into music. The original idea for this project came from R. D. King at the University of Wales, Aberystwyth and C. G Angus from the Shamen (King, R.D. & Angus, C.G. (1996)).


Platforms: Mac

t2prhd is a Perl script which generates simple diagrams that highlight relationships of sequence repeats detected by using a profile HMM in two sequences. Homology relations are identified on the basis of the phylogeny of repeats.


Platforms: *nix

django-ticketing also supports multiple sequences, which allows one to have sequences of tickets that are independent. This means you could have a sequence for users, a sequence for posts and a sequence for widgets. This is configured through your Django settings configuration.


Platforms: *nix

Fast5 is a probabilistic file format for the storage of nucleotide and protein sequences based on hdf5.


Platforms: *nix

CLC Protein Workbench is a scientific application for bioinformation, aimed at the advanced analysis of protein sequences. This program offers you a really wide range of analyses, all of them integrated in the same interface, which is very friendly and accessible to all users.The options and...


Platforms: Windows

Convert::GeekCode is a Perl module that can convert and generate geek code sequences. SYNOPSIS use Convert::GeekCode; # exports geek_decode() my @out = geek_decode(q( -----BEGIN GEEK CODE BLOCK----- Version: 3.12 GB/C/CM/CS/CC/ED/H/IT/L/M/MU/P/SS/TW/AT d---x s+: a-- C++++ UB++++$ P++++$...


Platforms: *nix

Term::ANSIScreen is a Perl module for terminal control using ANSI escape sequences. SYNOPSIS # qw/:color/ is exported by default, i.e. color() & colored() use Term::ANSIScreen qw/:color :cursor :screen :keyboard/; print setmode(1), setkey(a,b); print "40x25 mode now, with a mapped to...


Platforms: *nix

fl0p is a passive L7 flow fingerprinter that examines TCP/UDP/ICMP packet sequences. It can also can peek into cryptographic tunnels, can tell human beings and robots apart, and performs a couple of other infosec-related tricks. This approach differs from the techniques used by most other...


Platforms: *nix

MyCGR is an Objective-Caml library and a collection of tools to use the Chaos Game Representation on DNA sequences. MyCGR can empirically check the level and power of the tests and apply them on DNA sequences. It can generalize the dinucleotide abundance profile to a CGR-based relative...


Platforms: *nix

LiteSQL is a C++ library that integrates C++ objects tightly to relational database and thus provides an object persistence layer. LiteSQL supports SQLite3, PostgreSQL and MySQL as backends. LiteSQL creates tables, indexes and sequences to database and upgrades schema when needed. In addition to...


Platforms: *nix

Tk::event contains miscellaneous event facilities: define virtual events and generate events. SYNOPSIS $widget->eventAction(?arg, arg, ...?); The eventAction methods provides several facilities for dealing with window system events, such as defining virtual events and synthesizing events....


Platforms: *nix

Algorithm::Combinatorics Perl module is an efficient generator of combinatorial sequences. SYNOPSIS use Algorithm::Combinatorics qw(permutations); my @data = qw(a b c); # scalar context gives an iterator my $iter = permutations(@data); while (my $p = $iter->next) { # ... } # list...


Platforms: *nix

The ProtParam widget computes physico-chemical parameters for your protein sequences at ExPASy. You just have to type or paste your sequence in the input field.


Platforms: Mac

Serial Cloner is a light molecular biology software. Serial Cloner reads and write DNA Strider-compatible files and import and export files in the universal FASTA format (as well as in pDRAW32 format). Powerful graphical display tools and simple interfaces help the analysis and construction steps...


Platforms: Mac

The TweenMotif application was developed to be an interactive Windows program for visualizing the locations of a specified target motif within a set of sequences, as well as the gaps between the repeating motifs. The program creates a summary table of the frequency counts of the gap sequences...


Platforms: Windows

The usual way to demonstrate saturation in nucleotide sequences is to plot the fraction of differences between sequences against the evolutionary distance separating them. When the number of observed differences, for example for the fraction of third codon positions, no longer increases with...


Platforms: Windows

Recodon is a population genetic simulator that generates samples of nucleotide and codon sequences from populations with recombination, migration and growth. The last version includes new codon models (M1, M7 y M8) and new output options.


Platforms: Windows