BETRAN LAB

Evolutionary Biology

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SOFTWARE

The software and its accompanying documentation are provided as-is, without warranties of any kind. In general, all information presented in these pages and all items available for download are for public use. However, you may encounter some pages that require a login password and id. If this is the case you may assume that information presented and items available for download therein are for your authorized access only and not for redistribution by you unless you are otherwise informed.
It is in no way a complete list nor an indication of the availability of software for a given computer platform.

[Software Repositories] [Genetic Analysis Software][Graphing and Statistical Analysis Software] [Image Analysis Software] [Mathematical Software] [Molecular Modeling Software][PCR Software] [ Phylogeny Software] [Protein Structure Prediction Software] [Sequence Analysis Software] [Graphic Tools Software]

Software Repositories

Art's Biotech Resource Gateway Link to a number of biotech sources. Software is categorized into Mac, PC and Unix formatted programs.
BioCatalog The BioCatalog at EBI.
Bioperl Project A collection of Perl modules for analyzing and manipulating biological sequences and computational molecular biology.
CIT: Center for Information Technology CIT supports NIH's research and management programs provides links to a variety of molecular biology and bioinformatics sites.
EBI's ftp
Genamics is a repository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry.
IUBio A link to software for molecular biology and related areas.
Molecular Biology Software This page offers a small array of biotechnology related programs.
NMR Software This page introduces a multitude of software for various NMR duties.
Phylogenetic Analysis Computer Programs This site contains a list of tree inference, alignment, character evolution, and tree studies.
The Sanger Centre A collection of shareware and freeware sequence analysis programs.

Phylogeny Software

ANCML estimates ancestor states for a continuous trait, and provides a "standard error" for the marginal distribution of each estimate.
BIONJ A phylogenic reconstruction algorithm, which uses an improved version of the NJ algorithm, and is well adapted when evolutionary distances are obtained from aligned sequences.
CERVUS A program for likelihood-based parentage inference using codominant marker data. It can be used to calculate allele frequencies, run simulations to determine critical values of likelihood ratios and analyse parentage in populations of animals and plants.
Cluster A clustering program that uses single and complete linkage methods to determine the heirarchial clustering for a given data set.
DAMBE Data Analysis in Molecular Biology and Evolution.
DnaSP The analysis of DNA polymorphism for nucleotide sequence data.
GeneTree A program for comparing gene and species trees.
K-Estimator It estimates the number of nucleotide substitutions per site and the confidence intervals.
MacClade The analytical strength of MacClade is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts.
MALIGN A program for the alignment of molecular sequences based on the most parsimonious tree that can be constructed by the program algorithm.
MEGA Molecular Evolutionary Genetics Analysis.
PAML Phylogenetic Analysis by Maximum Likelihood. A program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
PASSML Phylogeny and Secondary Structure using Maximum Likelihood.
PAUP Phylogenetic Analysis Using Parsimony.
PHYLIP PHYLogeny Interference Package. Evolutionary trees. In this program, phylogenies are inferred by type of data or algorithm.
Phylodendron is an application for drawing phylogenetic trees.
PHYLTEST Allows a comparison of phylogenic trees, estimation of the pairwise distances, relative rate tests, and computation of the time of divergence.
Phylo Win A phylogeny analysis package with a user-friendly graphic interface.
PUZZLE reconstructs phylogenetic trees from molecular sequence data by maximum likelihood.
Quercus A program for the maximum likelihood analysis of variance of quantitative genetic data. The programs perform ML or REML on a two generation pedigree with multivariate phenotypic observations and fixed effects.
RAPDistance Records and fragment data can be analyzed in order to determine phylogeny.
RSTCALC A program for performing analyses of population structure, genetic differentiation and gene flow using microsatellite data. RSTCALC calculates unbiased estimates of RST and assesses their significance using bootstrap and permutation tests.
SplitsTRee An interactive program for analyzing and visualizing evolutionary data. Based on the split decomposition method this program takes input as a distance matrix or a set of aligned sequences and produces as output a graph that represents the evolutionary relationships between taxa.
Treemap TreeMap is a program for comparing host and parasite trees.
Treeview A simple program for displaying phylogenies that reads standard NEXUS and PHYLIP formatted trees.
VORTEX is for population viability analysis.

PCR Software

GPRIME helps with the design of PCR primers for an aligned group of related nucleotide sequences.
Primer3 is for designing primers.

Sequence Analysis Software

AMAS: Analyze Multiple Alignments of Protein Sequences Allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree.
Artemis is a DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.
BASS A software program for tracking, extracting, and base calling DNA sequencing gels.
BOXSHADE A program that uses preprocessed multiple alignment files as input to produce printouts of aligned protein or DNA sequences.
Chromas displays and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files and it allows the user to manipulate the sequences.
CINEMA Colour INteractive Editor for Multiple Alignments allows the visualization and manipulation of both protein and DNA sequences.
ClustalW is a popular and improved multiple alignment program for DNA or proteins.
ConsInspector Predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. These consensus descriptions produced by the program ConsInd consist of the length of the binding site and the individual conservation of each nucleotide position within the site.
Coresearch is used to identify and delimitate consensus elements (e.g. protein binding sites) in a set of unaligned nucleic acid sequences.
Delila is for information analysis of protein and nucleic-acid sequences.
DIALIGN is a multiple sequence alignment program that compares whole segments rather than single residues.
DNA Strider full featured sequence manipulation application for the mac.
DomainFinder determination and characterization of dynamical domains in proteins.
Dotter A dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis.
gBioSeq Sequence editor for GTK/Linux.
Geanfammer summarises the whole procedure of preparing statistically and biologically more relevant protein (sequence) duplication modules of bacterial genomes.
GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support.
HMMER A profile hidden Markov model tha can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
LalnView A graphical program for visualizing local alignments between two sequences for proteins and nucleic acids.
MacStripe is an ideal tool for anyone who wants to explore potential alpha-helical coils in the sequence of their protein.
MatInspector Matches in sequences of unlimited length are located by this program.
MEME Discovers motifs (highly conserved regions) in groups of related DNA or protein sequences using MEME and searches sequence databases using motifs using MAST.
ModelGenerator and ModelInspector Develops functional models for transcriptional regulatory DNA units.
Mutability A program which takes a DNA sequence and determines how many single point mutations would result in nonsense, missense, or neutral mutations.
Pfam A database of multiple alignments of protein domains or conserved protein regions.
Pratt Discovers patterns conserved in sets of unaligned protein sequences.
Promotif Analyzes a protein coordinate file and provides details of the structural motifs in the protein.
RepeatFinder Perl source code that searches for DNA/protein sequence repeats.
SAM: Sequence Alignment and Modeling System A hidden Markov modeling suite software system.
SeaView This is a multiple sequence alignment editor.
SeqPup A biosequence sequence editor and analysis program for multiple sequence alignments and single sequence editing.
webblast A perl program that conducts NCBI blast searches by acting as a www client like Netscape or Internet Explorer. The program saves results as local files in HTML or plain text.
Wise2 A software package that compares DNA sequences at the level of conceptual translation, regardless of sequencing error and introns. It can compare a single protein or a profile HMM to a genomic DNA sequence, and predict a gene structure.
WU-BLAST is for gene and protein identification through sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases.
XYLEM A collection of tools designed enable the user to identify, extract and manipulate data from major databases such as GenBank, EMBL and PIR.

Protein Structure Prediction Software

Aqua A suite of programs for analyzing the quality of biomolecular structures that were determined via NMR spectroscopy.
DICROPROT a package of methods designed for the estimation of protein sequence secondary structure.
DomainFinder A program for the determination and characterization of dynamical domains in proteins.
DOWSER The Dowser program surveys a protein molecule's structure to locate internal cavities and assess the hydrophilicity of these cavities in terms of the energy of interaction of a water molecule with the surrounding atoms.
FAMBE: Fast Adaptive Multigrid Boundary Element method A program written to calculate the solvation energy of a solute molecule in a solvent. The calculation is based on the dielectric continuum model with which it is possible to calculate the free energy of polarization of the solvent by the charges of the solute molecule.
Macromolecular Geometry A library of source code for doing a variety of calculations on protein structures and sequences.
MODELLER A program for homology protein structure modelling by satisfaction of spatial restraints.
PROCHECK Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.
pSAAM Assists in analysis of protein sequences for information aboutsecondary and tertiary structure.
SARF2 A program for spatial arrangement of backbone fragments in protein structures.
SIMS: Smooth Invarient Molecular Surface A program written to calculate the molecular surface which envelops the solvent-excluded volume of the solute molecule. The SIMS calculates a DOT presentation of the molecular surface, an array of 3D coordinates of surface elements, their normal vectors and areas.
STAMP A suite of programs for the comparison and alignment of protein three dimensional structures. The suite will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position.
TOP A program which compares protein structures and performs 3d database searching via the internet.
Vienna RNA Package A package for RNA secondary structure prediction and comparison consisting of a code library and several stand-alone programs for prediction and comparison.

Molecular Modeling Software

ARP/wARP A program for the refinement of protein structures that combines in an iterative manner the reciprocal space structure factor refinement with updating of the model in real space.
Chime This program is used to view molecular structures on Netscape.
Cn3D This 3D molecular structure viewer for data entries from Entrez, allows the rotation of structures.
DOCK addresses the problem of "docking" molecules to each other. It explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together.
Espoir A special purpose Reverse Monte Carlo code for ab initio crystal structure determination.
FTDOCK A program that performs rigid-body docking on two biomolecules in order to predict their correct binding geometry.
GRASP This tool is designed to facilitate the study of macromolecular function by mapping a number of structural, chemical, and biological properties onto various representations of molecular structure (molecular surfaces, wire frame, CPK spheres, or backbone tracing ribbons).
GROMOS This is a general-purpose molecular dynamics simulation package.
Kinemage A package of 2 programs (Prekins and Mage) that enables the user to create a 3D image from a PDB-format coordinate file, which then can be modified.
LIGPLOT A program for automatically plotting protein-ligand interactions. The interactions shown are those mediated by hydrogen bonds and by hydrophobic contacts.
loopDloop This is a tool for drawing RNA secondary structures.
MidasPlus An advanced molecular modeling system that display and manipulate macromolecules such as proteins and nucleic acids.
MINT is a graphical user interface to Andrej Sali's Modeller program. It allows only the basic homology modelling functions of Modeller to be used, but saves you from having to use the Modeller control language.
MOIL-View may be used to view and analyze molecular structures and dynamics.
MOLDEN A package for the visualization of molecular and electronic structure.
MOLMOL 2.4 A program for the analysis and display of molecules.
MolScript A program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces. This program is written in C programming language and can be used as a standalone program or as an AVS (Advanced Visualization System) module. Binary versions of MSMS are available for SGI, Dec Alpha, HP9000 and Sun workstations.
MSV is an OpenGL based viewer for molecular surfaces computed with MSMS.
NAB: Nucleic Acid Builder A computer language for modelling nucleic acids, which allows description in a heirarchial fashion.
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. The software is available via anonymous ftp.
NAMOT2: Nucleic Acid MOdeling Tool A graphic tool to build and manipulate nucleic acid structures.
NUCPLOT A program that generates schematic diagrams from 3D coordinates found in a given PDB file. The program works for single and double stranded proteins, DNA, DNA-ligand, and protein-RNA complexes.
The O Files A general purpose macromolecular modelling program aimed at the field of protein crystallography. It enables the scientist to model, build and display macromolecules.
ORTEP-III A thermal ellipsoid plot program for crystal structure illustrations.
Oscail A software system for solving, refining and examining small molecule crystal structures.
Phases A package of computer programs designed to compute phase angles for diffraction data from macromolecular crystals. The package contains programs for merging and scaling of native and derivative data sets, analyzing difference statistics, computing Patterson and electron density maps, and various isomorphous replacement routines.
QTree A program for generating space-filling models from PDB files. It is capable of generating worms and ball-and-stick models as well as using preprocessing filters.
RasMol is intended for visualization of proteins, nucleic acids, and small molecules. .
SIgMA: SImulations of MAcromolecules A program for conducting energy minimization, free molecular dynamics, constrained and restrained molecular dynamics, and molecular dynamics with free-energy methods.
SPOCK Molecular graphics software including several bond and atom rendering types, a complete array of backbone "worm" representations, can calculate and display molecular and accessible surfaces and color code these surfaces by properties.
STING A tool for the simultaneous display of information about macromolecular structure (in STING's Graphics Frame) and sequence (in STING's Sequence Frame). Special attention is given to MacroMolecular INTERFACE analysis.
SURFNET Generates surfaces and viod regions between surfaces from coordinate data supplied in a PDB file. It can compute: van der Waals surfaces; gaps between molecules; clefts, cavities and binding sites; 3D denisty distributions and sidechain interactions, and planes, paraboloids and boxes.
Swiss-PdbViewer Application that provides an interface to analyse several proteins at the same time. Amino acid mutations, H-bonds, angles and distances between atoms are easily to obtained using the graphical user interface.
TINKER A molecular modeling software for molecular mechanics and dynamics, with some special features for polypeptides.
TOPS Generates protein topology cartoons. Places circles and triangles depicting alpha-helices and beta-strands respectively giving a pictorial topological summary of any protein structure.
VMD: Visual Molecular Dynamics Macromolecular structures such as proteins and lipid bilayer assemblies can be visualized and analyzed by this program.
WHAT IF This protein structure analysis program can be used for molecular graphics and structure verification.
XtalView The construction of x-ray crystal structures by the fitting of molecular models into an electron density map is possible with this program.

Genetic Analysis Software

AMPS A suite of programs for multiple sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures, and also implements flexible pattern matching and database scanning options.
Bioperl Software package for computational molecular biology.
CloneIt A program for use in plasmid cloning to quickly find in-frame deletions, sub-cloning, and frameshifts strategies.
CLUSTAL W is a multiple sequence alignment program for biological sequences.
Codontree is able to determine a codon usage table for a set of protein coding genes, gene relationship on the basis of codon usage similarity, and compositional features of protein coding genes.
createGel Perl source code that creates a gel project out of blast results. To be used in conjunction with splitblast.
Flip A Unix C program used to find and translate orfs. Flip reformats DNA sequences and produces output files that can be used by other programs such as FASTA.
Gassoc This software makes disease and genetic marker associations using cases and their parents.
GeneMark is used for gene prediction in sequences.
Genome Inspector This tool detects distance associations between sequence elements.
Glimmer A system for finding genes, using interpolated Markov models to identify the coding regions and distinguish them from noncoding regions, in microbial DNA (especially the genomes of bacteria and archaea)
Image is a package of analysis algorithms for processing gel images from restriction digest fingerprinting.
JaMBW 1.1: Java based Molecular Biologist's Workbench A collection of programs designed to exploit the most common bioinformatic operations that a molecular biologist currently has, including manipulation and analysis of DNA sequences.
MSA A program to do multiple sequence alignment under the sum-of-pairs criterion.
QTL Cartographer This tool maps quantitative traits using a map of molecular markers.
SCANPS A local alignment method to search protein sequence databases with a query sequence or multiple alignment, and also allows all pairwise comparisons to be made between a set of sequences and can estimate the statistical significance of the alignments.

Image Analysis Software

ALP Automated Linkage Preprocessor. Determines sizes of microsatellite fragments separated on an A.L.F. Sequencer (Pharmacia Biotech), removes stutter, performs genotyping and Mendelian checks, and formats data for Lathrop's Linkage Program Package.
NIH Image Digital image analysis package - used for signal quantification and determining relative intensities of bands etc.

Graphing and Statistical Analysis

Dynafit Dynafit makes nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data.
NLREG: NonLinear REGression analysis program performs linear and nonlinear regression analysis and curve fitting. NLREG can handle linear, polynomial, exponential, logistic, periodic, and general nonlinear functions.

Mathematical Software

Decision Tree for Optimization Software This site aims at helping you identify ready to use solutions for your optimization problem, or at least to find some way to build such a solution using work done by others.
Derive
Diffpack is an object-oriented development framework for multi-physics simulation.
GAP
Graphics and analysis software
Guide to Available Mathematical Software A cross-index and virtual repository of mathematical and statistical software components of use in computational science and engineering.
LASPack
Magma is a large, well-supported software package designed to solve computationally hard problems in algebra, number theory, geometry and combinatorics.
Mathcad
Mathematica
Mathematica Related URL's
Mathematics Archives
Mathlab
Matrix Market
Minitab
Octave GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.
VisSim Dinamic modeling and simulation software.

Graphic Tools

Graphics Workshop This workshop allows an individual to view, manipulate, and manage graphics.
Lview Pro Lview Pro is an image viewer and editor with JPEG support.
NcView A visual browser for netCDF-format files.
NIH Image Acquires, displays, edits, enhances, analyzes and animates images. It can be used to measure area, mean, centroid, perimeter, etc. of user defined regions of interest. It also performs automated particle analysis and provides tools for measuring path lengths and angles.
OSIRIX A general medical image manipulation and analysis software designed for physicians and non computer-oriented users.
PDBViewer Swiss-PdbViewer can load and display several molecules simultaneously.
PiXCL Tools This is a 2D graphics, image display and processing language toolkit and EXE builder.
Scion Image Can acquire, display, edit, enhance, analyze and animate images. It can be used to measure area, mean, centroid, perimeter, etc. of user defined regions of interest. It also performs automated particle analysis and provides tools for measuring path lengths and angles.
ShadyBox This drawing program enables boxing and shading of regular and irregular shaped segments of aligned multiple sequences.


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