Nucleotide

Nucleotide BLAST Widget provides a quick access to the Nucleotide Basic Local Alignment Search Tool at NCBI. You just have to type or paste your sequence and to select the program to be used.

inGAP is a handy, easy to use application specially designed to offer you an integrative next-generation genome analysis pipeline, which employed a Bayesian principle to detect single nucleotide polymorphisms (SNPs), small insertion/deletions (indels). inGAP has been applied to a number of genome...

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

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


Platforms: *nix

A minimalistic tool for molecular phylogenetics able to recover phylogenies from nucleotide sequences. PhyloCoco uses the likelihood or the minimum evolution criterion, and automatically selects the best substitution model of DNA evolution for the dataset analyzed.PhyloCoco key-features are: -...


Platforms: Mac

VCAKE is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina's Solexa Sequencing data.


Platforms: Windows, Mac, Linux

Design primers based on length, melting temperature, GC content, hairpins, dimerization, nucleotide repeats, and 3' GC clamp criteria.Import data from files or from Genbank.


Platforms: Matlab

Virusbanker is a MySQL database of virus sequences and alignments that is accessed via a Java program. To use the database you need to download the Java program. The program creates an interface with three spreadsheets and a selection menu. We describe the process of setting up VirusBanker below;...


Platforms: Mac

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: * Is flexible enough to store all the alignment information generated by various alignment programs; * Is simple enough to be easily generated by alignment...


Platforms: Mac

SIMMAP 1.5 is a post tree analysis GUI software package for stochastically mapping mutations on phylogenies. This approach does not rely on parsimony and, therefore, does not suffer some of the serious drawbacks of that method. It uses the "indirect" mutational mapping approach as first developed...


Platforms: Mac

jMOTU is a software package for clustering barcode DNA sequence data into molecular operational taxonomic units (MOTU). If you are not sure what a MOTU is, please see the DNA Barcoding pages on our website. jMOTU does the following: *reads input sequences in FASTA or NEXUS format *calculates...


Platforms: Mac

SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools. Background Deluged by the rate and complexity of completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus been developed. In the...


Platforms: Mac

This script takes genotypes from two different arrays and creates a consensus spreadsheet, and two optional spreadsheets. In order to run this script two spreadsheets of mapped genotype data are required. The spreadsheets may also contain non-marker mapped columns as they will be skipped when...


Platforms: Mac

pknotsRG is a tool for folding RNA secondary structures, including the class of simple recursive pseudoknots. The program runs in O(n^4) time and O(n^2) space, therefore its application here on the BiBiserv is limited to sequences of length up to 800 bases. The energy parameters for structures...


Platforms: Mac

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision...


Platforms: Mac

R'MES finds the expected and actual frequencies of short nucleotide sequences, or words, using a Markov model to control for the effects of base composition and the frequencies of shorter words. Unusually frequent or infrequent occurrences of certain words may indicated biological relevance. For...


Platforms: Mac

ToBiX is a Morphix-based Linux live CD containing a range of specialist applications for bioinformatics. With this distrubution you just boot from the CD and you have a fully functional LINUX OS distribution with open source applications. Besides using some RAM, ToBiX doesnt touch the host...


Platforms: *nix

Bio::Tools::CodonTable is a bioperl codon table object. SYNOPSIS # This is a read-only class for all known codon tables. The IDs are # the ones used by nucleotide sequence databases. All common IUPAC # ambiguity codes for DNA, RNA and animo acids are recognized. # to use use...


Platforms: *nix

CLC Free Workbench is the foundation for all bioinformatics workbenches from CLC bio. This software package is a community edition, available for download free of charge.The workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management,...


Platforms: Mac