Amino Acids

CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. It was written in ANSI compliant C. See the README file for more information.

BATE calculates pH of solutions containing mixtures of acid and base with up to 4 dissociation steps and titration curves for these acids and bases. Ionic strentgh can be calculated, omitted or forced. Program contains editable database of common weak acids and bases and accepts acid and base...

BATE calculates pH of solutions containing mixtures of acid and base with up to 4 dissociation steps and titration curves for these acids and bases. Ionic strentgh can be calculated from the dissociated forms concentrations, omitted or forced upon the solution. Program contains editable database...


Platforms: Windows

The DNA Molar Converter widget is a Dashboard widget that allows to perform molar conversions for nucleic acids according to size.


Platforms: Mac

The FastPCR software was developed to be an integrated tools environment that provides comprehensive facilities for designing primers for most PCR applications including standard, long distance, inverse, real-time, multiplex, unique and group-specific; overlap extension PCR (OE-PCR)...


Platforms: Windows, XP, 2003, Windows Vista, XPX64, 7, 7x64

A pH Calculator, a Virtual Titrator, a Real Titration Data Analyzer, a Distribution Diagram Generator - that's CurTiPot, the all-in-one freeware to learn, teach and work with chemical equilibrium of acids, bases, salts and buffers at home, classroom, interactive "dry lab", routine or research...


Platforms: Windows

Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.


Platforms: Windows, Mac, Linux

BASILISK is a probabilistic model of the conformational space of amino acid side chains in proteins. Unlike rotamer libraries, BASILISK models the chi angles in continuous space, including the influence of the protein's backbone.


Platforms: Mac, Linux

BiasViz is a Java applet for visualization of amino acid bias in multiple sequence alignments.


Platforms: Windows, Mac, Linux

CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. It was written in ANSI compliant C. See the README file for more information.


Platforms: Windows, Mac, BSD, Linux

iso2l (ˈaisəutuːl, spoken isotool) is a software to calculate the isotopic distribution of a chemical formula or a amino acid chain.


Platforms: Windows, Mac, Linux

MatrixGen is a Bioinformatics application used to generate scoring matrices from analysis of aligned Amino Acid and DNA data sets. These matrices can then be used by Clustal to generate more accurate alignments. Based upon the Henikoff BLOSUM method.


Platforms: Windows, Mac, BSD, Linux

Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.


Platforms: Windows, Mac, Linux

ProDy is a free and open-source Python package for analyzing protein structural dynamics. It allows for quantitative analysis of heterogeneous experimental structural datasets and comparison with theoretically predicted conformational dynamics. The input for ProDy is the atomic coordinates of...


Platforms: *nix

CurTiPot pH & Acid-Base Titration Curves. A powerful all-in-one freeware for pH calculation, experimental data analysis and simulation of titration curves of acids, bases, salts and buffers (from simple solutions to complex mixtures), with interpolation, smoothing and nonlinear regression....


Platforms: Windows

Bio::Tools::Run::PiseApplication::charge is a Perl module. Bio::Tools::Run::PiseApplication::charge Bioperl class for: CHARGE Protein charge plot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/charge.html for available values): charge (String) init...


Platforms: *nix

MassSpec::CUtilities is a Perl extension containing C utilities for use in mass spectrometry. SYNOPSIS MassSpec::CUtilities is an XS module so theres a chance that you or your target user might not get it to install cleanly on the target system; therefore its recommended to make its presence...


Platforms: *nix

Bio::AlignIO::bl2seq is a bl2seq sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class, as in: use Bio::AlignIO; $in = Bio::AlignIO->new(-file => "inputfilename" , -format => bl2seq); $aln = $in->next_aln(); This object can create...


Platforms: *nix

biOpen is a new and unique DNA and protein sequence analysis and structure visualization software based on dynamic integration of analysis tools. This evaluation version includes the interactive multiple trace view, the Documentation window, DNA/RNA analysis tools (including Contig Assembly),...


Platforms: Mac

Structure is a screensaver for Mac OS X that draws on the National Center for Biotechnology Information's protein databases to display beautiful 3D protein structures on your screen. It ships with about ten sample structures and via the Internet has seamless access to a database of tens of...


Platforms: Mac