Bibus

here

Endnote

here

Bibus is a bibliographic and reference management software. As with other such tools, Bibus allows one to search, edit, and sort bibliographic records; some more exclusive features available

ccleaner

here

Registry Cleaner

here

CCleaner is a freeware system optimization, privacy and cleaning tool. It removes unused files from your system - allowing Windows to run faster and freeing up valuable hard disk space. Fully featured registry cleaner.

Chicken of the VNC

here

n/a

n/a

Chicken of the VNC is a VNC client for Mac OS X. A VNC client allows one to display and interact with a remote computer screen. In other words, you can use Chicken of the VNC to interact with a remote computer as though it's right next to you.

Clustal

here

n/a

here

Multiple alignment of nucleic acid and protein sequences

DAMBE

here

Sequencher and/or PAUP

n/a

1. Sequence alignment * General sequence alignment with nucleotide and amino acid sequences * Aligning protein-coding nucleotide sequences against aligned amino acid sequences 2. Molecular phylogenetics * Distance-based methods including neighbor-joining, Fitch-Margoliash, FastME and UPGMA, in conjuction with a variety of genetic distances including simultaneously estimated maximum composite likelihood distances, as well as a variety of distances based on nucleotide, amino acid and codon based substitution models. * Maximum parsimony methods * Maximum likelihood methods * A versatile tree-displaying panel for exporting high-quality trees for publication * Relative rate tests with nucleotide-based and codon-based models * Tree-based test of the molecular clock hypothesis * Estimation of o the shape parameter of the gamma distribution for rate heterogeneity o the proportion of invariate sites * Test substitution saturation * Find best-fitting substitution models 3. Bioinformatics tools * Position weight matrix for characterizing and predicting sequence motifs * Perceptron for two-group classification of sequence motifs * Gibbs sampler for characterizing and predicting novel/hidden sequence motifs * Hidden Markov models * Secondary structure prediction * tRNA anticodon identification * Characterization of codon usage bias with RSCU and CAI * Computing protein isoelectric point * Peptide mass fingerprinting 4. Extensive implementation of a variety of sequence formats, from the simplest FASTA format to the annotation-rich GenBank format. With the GenBank format, one can easily extract coding sequences (CDSs), exons, introns, exon-intron junctions, rRNA, tRNA, sequence upstream or downstream of CDSs, and many others.

EMBOSS

"The European Molecular Biology Open Software Suite"

here

n/a

here

A specially developed application for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web.

Filezilla

here

n/a

here

FTP client. It supports FTP, SFTP, and FTPS (FTP over SSL/TLS).  Transfer files between computers and/or servers.

Firefox

here

Internet Explorer

here

Mozilla Firefox is a free and open source web browser. Functions can be added through add-ons created by third-party developers, including FTP clients, tab organization, and many great other ones.

Foxit reader, editor, and creator

here

Adobe Acrobat Reader Professional

here

As a small and fast PDF viewer and editor, Foxit Reader features new features, such as multimedia design and Foxit OnDemand Content Management and is the first and still the only REAL editor for PDF files.

GRASS

"Geographic Resource Analysis Support System"

here

ArcGIS

here

Commonly referred to as GRASS, this is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization.

GIMP

"GNU Image Manipulation Program"

here

Photoshop

here

photo retouching, image composition and image authoring. It has many capabilities. It can be used as a simple paint program, an expert quality photo retouching program, an online batch processing system, a mass production image renderer, an image format converter, etc. GIMP is expandable and extensible. It is designed to be augmented with plug-ins and extensions to do just about anything.

Izarc

here

Windows Archiver

here

IZArc is the best freeware archive utility supporting many archive formats like: 7-ZIP, A, ACE, ARC, ARJ, B64, BH, BIN, BZ2, BZA, C2D, CAB, CDI, CPIO, DEB, ENC, GCA, GZ, GZA, HA, IMG, ISO, JAR, LHA, LIB, LZH, MDF, MBF, MIM, NRG, PAK, PDI, PK3, RAR, RPM, TAR, TAZ, TBZ, TGZ, TZ, UUE, WAR, XXE, YZ1, Z, ZIP, ZOO. With a modern easy-to-use interface, IZArc provides support for most compressed and encoded files, as well as access to many powerful features and tools.

LEd (LaTeX Editor)

here

n/a

here

LEd (LaTeX Editor) is a free environment for rapid TeX/LaTeX document processing. Our main goal in developing the editor is to make the process of TeX/LaTeX document production easier thanks to the integration of the most helpful tools into one application.

Lyx

here

n/a

here

LyX is a document processor that encourages an approach to writing based on the structure of your documents (WYSIWYM) and not simply their appearance (WYSIWYG). LyX combines the power and flexibility of TeX/LaTeX with the ease of use of a graphical interface. This results in world-class support for creation of mathematical content (via a fully integrated equation editor) and structured documents like academic articles, theses, and books. In addition, staples of scientific authoring such as reference list and index creation come standard. A broad array of ready, well-designed document layouts are built in. LyX is for people who want their writing to look great, right out of the box. No more endless tinkering with formatting details, “finger painting” font attributes or futzing around with page boundaries. You just write. On screen, LyX looks like any word processor; its printed output — or richly cross-referenced PDF, just as readily produced — looks like nothing else.

NetBeans

here

Visual Studio

here

Integrated Development Environment for software developers. You get all the tools you need to create professional desktop, enterprise, web, and mobile applications with the Java language, C/C++, and even dynamic languages such as PHP, JavaScript, Groovy, and Ruby.

NVU and KompoZer

here

Dreamweaver

here

Nvu is a graphical webpage editor and mamagement tool. A complete web authoring system.

Open Office Suite

here

Microsoft Office

here or here

OpenOffice is the leading office software suite  for word processing, spreadsheets, presentations, graphics, databases and more. It is available in many languages and works on all common computers. Can open most file types.

Opera

here

Internet Explorer

here

Web browser with e-mail client and available add-ons

PDF creator

here

n/a

n/a

print or save any document straight to PDF

Programmers Notepad

here

n/a

here

powerful text editor featuring syntax highlighting, project management, a great user interface, etc.

Quantum GIS

here

ArcView(?)

here

Open source GIS program especially useful for visualization, management, editing, and data analysis, as well as composition of maps.

R

here

S, S-Plus, but can also be used instead of SAS

here

A powerful statistics program which can be used for very many different kinds of analyses and features contributed packages specialized for biological analyses (in all specializations). Among others, it can be used for most ecological and molecular analyses. Genbank sequences can be downloaded directly into R and processed with certain packages. Please visit the CRAN website for all available uses.

Seamonkey

here

Netscape(?)

here

Web-browser, advanced e-mail and newsgroup client, IRC chat client, and HTML editing and development suite ... all in one application.

Songbird

here

Windows media player

here

customizable media player opening many different formats

SSH

here

Secure Shell Client

here

(access other computers by command line and transfer files between mashines)

Sunbird

here

n/a

here

full-featured and easy to use calendar application that you can use around the world.

Thunderbird

here

Microsoft Outlook

here

Cross-platform e-mail client with enterprise and government-grade security features.

TightVNC

here

RealVNC

here

Access lab computers and work on them from home or anywhere else in the world. See the desktop of a remote machine and control it with your local mouse and keyboard, just like you would do it sitting in the front of that computer.

Bioinformatics Links Directory

here

The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. The links listed in this directory are selected on the basis of recommendations from bioinformatics experts in the field.

Molecular Biology Freeware for Windows

here

A number of useful Molecular Biology Tools, both online and downloadable programs. A few examples are: microaaray software, plasmid graphics, phylogeny, protein analysis, and primer design.

Phylogeny Programs

here

Here are 386 phylogeny packages and 52 free servers, all that I know about. It is an attempt to be completely comprehensive. I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made roughly weekly. Here is a "waiting list" of new programs waiting to have their full entries constructed. Many of the programs in these pages are available on the web, and some of the older ones are also available from ftp server machines.

The Bio-Web Software for Mac

here

Software for molecular biology, especially for Macintosh computers. Examples are amplification, plasmid, sequence alignment, and other software.

Biotech Resource Software

here

A list of free software useful to Molecular Biology and Structural Biology Fields.

Mac Programs for Animal Behavior

here

page describes and provides access to three Macintosh programs that may be of use to researchers in animal behavior or field ecology

Clearinghouse for Ecology Software

here

A clearinghouse for a diverse group fo ecology programs, including some for home ranges, population ecology, bioacoustics, ecological statistics, etc.

Open Directory Project - Biology

here

This page contains a wide variety of biology programs (ecology to molecular biology), as well as lists of suppliers, certain publications, methods and techniques, and even jokes =)

Statpages

here

A list of tutorials, help with statistics, as well as links to free statistics software and scripts for such programs as R, SAS, S, and S-Plus

StatSoft

Online Statistics Book

here

A great online statistics book covering large grounds from the simplest definitions to multivariate and non-parametric analyses in statistics.

Statistical Software Sites

here

A huge collection of statistical software (both online and downloadable), as well as help sites, etc.

SourceForge

here

A website featuring thousands of free programs for any kind of task.

Free Software Directory

here

Large Depository of free and open source software for biology and everything else

Cuil

here

An alternative to google search engine. Ad free and to a large degree less cluttered

GIS Data Depot

here

A depot for nation-wide US geospatial data

RGIS

here

New Mexico Resource Geographic Information System Program - provides access to data, training, and technical support for geographic information users, as well as those who desire to incorporate geographic information into their processes and applications.