Software

		Avian Influenza Virus Genomics and Bioinformatics Workshop August 6-11, 2007, Hosted at Hanoi School of Public Health, Hanoi, Viet Nam

Software:

Go to: Software directory
Go to: General Purpose Software
Go to: Selected Bioinformatics Software

* Note: all software are only available on the DVD for the class workshop and on the local workshop web server and NOT on the bioinfohelpdesk.org site. Use the link to the online resource to download the latest version.

General Purpose Software:

Text Editors:
- ConTEXT Programmer Editor version 0.98.4 [1.59MB]- (ConTEXTsetup_v0_98_5.exe) 2006/Dec/03: http://www.context.cx/ - FREE
- TextPad 4.7.3 (txpeng473.exe Evaluation version) June 17, 2004 - is "a powerful, general purpose editor for plain text files. Easy to use, with all the features a power user requires." http://www.textpad.com/ - Very powerful - Trial
- NotePad Plus Plus (npp.4.0.2.Installer.exe) - Notepad++ is a free source code editor (and Notepad replacement), which supports several programming languages, running under the MS Windows environment. http://notepad-plus.sourceforge.net/uk/site.htm
Network Clients:
- WinSCP 4.0 beta [2007-Apr-07] (winscp400setup.exe)- WinSCP is an open source SFTP (SSH File Transfer Protocol) and SCP (Secure CoPy) client for Windows using SSH (Secure SHell). Its main function is safe copying of files between a local and a remote computer. http://winscp.sourceforge.net/eng/
- Putty release version (0.59 - released 2007-Jan-24) (putty.exe = For Windows 95, 98, ME, NT, 2000 and XP on Intel x86) - PuTTY is a free implementation of Telnet and SSH for Win32 and Unix platforms, along with an xterm terminal emulator. Simply: you run PuTTY on a Windows machine, and tell it to connect to (for example) a Unix machine. PuTTY opens a window. Then, anything you type into that window is sent straight to the Unix machine, and everything the Unix machine sends back is displayed in the window. So you can work on the Unix machine as if you were sitting at its console, while actually sitting somewhere else. It is written and maintained primarily by Simon Tatham. http://www.chiark.greenend.org.uk/~sgtatham/putty/
Utilities:
- WinZip (winzip90.exe) / (winzip100.exe)[45-day trial period]- Commercial Compression utility for MS Windows http://www.winzip.com/ . How to get WinZip for free? Other free zip utilities.
Office:
- OfficeOpenOffice.org 2.2.1 (yy-xxx2007) - (OOo_2.2.1_Win32Intel_install_wJRE_en-US.exe) [108.57 MB]-- OpenOffice.org is a free productivity suite compatible with all major office suites.- http://www.openoffice.org/
- Power Point Viewer 2007 (9-Nov-2006) - PowerPointViewer.exe [big 25.77 MB] - or online at Microsoft Office download
- Adobe Acrobat Reader 7.08 (AdbeRdr708_en_US.exe)-- All PDF files require a software to view and print Adobe Portable Document Format (PDF), either download the Adobe Reader or GSview
Browser:
- Mozilla Firefox 2 Windows (release Oct 24, 2006) (Firefox Setup 2.0.0.3.exe) - Web browser from Mozilla. http://www.mozilla.com/
Adobe Flash Player version 9,0,45,0 (date posted: April 12, 2007) (install_flash_player.exe) - needed to watch and listen to the lecture presentation. Read Flash Installation Note
Java(TM) SE Runtime Environment 6 Update 1- (jre-6u1-windows-i586-p.exe) - http://java.sun.com/javase/downloads/index.jsp - JRE is needed to run some Java applications.
- Prior version (JRE 5.0 Update 9): jre-1_5_0_09-windows-i586-p.exe (Java Runtime Environment)
- Even older Prior version: j2sdk-1_4_2_13-windows-i586-p.exe (Java Softwre Development Kit -- for developers, incl the Java Runtime Environment)

Selected Bioinformatics Software (Standalone and Web):

General Molecular Biology Packages:
- EMBOSS-MS (emboss-4.1.0-1-setup.exe) - A high-quality package of free, Open Source software for molecular biology. http://emboss.sourceforge.net/ and Download: ftp://emboss.open-bio.org/pub/EMBOSS/windows/
  - vcredist_x86.exe (for 32 bit version of Microsoft Windows) - The EMBOSS-MS version of EMBOSS may require that you install the Visual C/C++ 2005 runtime DLLs.
- NCBI Genome Workbench 0.15- (gbench-win2k-0.15.exe) NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data. http://www.ncbi.nlm.nih.gov/projects/gbench/
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Sequence Alignment: Pairwise:
NCBI standalone BLAST (Current: - blast-2.2.16-ia32-win32.exe Mar/25/2007) - perform BLAST searches locally. You provide both the query sequence(s) and database. Processing is local.

Documents: http://www.ncbi.nlm.nih.gov/BLAST/docs/
Download: ftp://ftp.ncbi.nih.gov/blast/executables/
~~Database sets may be retrieved automatically with update_blastdb.pl (local copy here)~~

NCBI netblast - (Current: netblast-2.2.16-ia32-win32.exe - Mar/25/2007) - perform BLAST searches using the servers and databases at NCBI . You provide the query sequence.
- Documents: http://www.ncbi.nlm.nih.gov/BLAST/docs/
- Download: ftp://ftp.ncbi.nih.gov/blast/executables/
Needle - global alignment - used to compare two sequences that covers the whole length of both sequences
- http://www.ebi.ac.uk/emboss/align/ (part of EMBOSS)
Water - local alignment - to find the best region of similarity between two sequences
- http://www.ebi.ac.uk/emboss/align/ (part of EMBOSS)
ProSplign - Protein-to-Genomic Alignment tool - used in the NCBI FLU Annotation Project
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Sequence Alignment: Multiple:
- ClustalX ver 1.83 for windows (clustalx1.83.zip Apr/17/2003 for MS Windows version and clustalx1.83.XP.zip Oct/1/2004= for MS Windows XP)- Clustal X is a new windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment - http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html and ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/
  - ClustalW 1.832 for windows -- command line version clustalw1.83.XP.zip
  - Web version: http://www.ebi.ac.uk/clustalw/
- T-Coffee
  - Web version: http://www.ebi.ac.uk/t-coffee/
- MUSCLE (muscle3.6_win32.zip) - is public domain multiple alignment software for protein and nucleotide sequences. MUSCLE stands for multiple sequence comparison by log-expectation.
  - Standalone version: http://www.drive5.com/muscle/
  - Web version of MUSCLE: http://phylogenomics.berkeley.edu/cgi-bin/muscle/input_muscle.py
  - Web version: http://www.ebi.ac.uk/muscle/
- Mafft - (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.
  Web version: http://www.ebi.ac.uk/mafft/
- Kalign - A fast and accurate multiple sequence alignment algorithm.
  - Web version: http://www.ebi.ac.uk/kalign/
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Alignment Editors
- BioEdit 7.0.5 updated May/31/2005 (BioEdit_7.05_20050531.zip) - BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP. An intuitive multiple document interface with convenient features makes alignment and manipulation of sequences relatively easy on your desktop computer. Several sequence manipulation and analysis options and links to external anaylsis programs facilitate a working environment which allows you to view and manipulate sequences with simple point-and-click operations- http://www.mbio.ncsu.edu/BioEdit/bioedit.html [http://www.mbio.ncsu.edu/BioEdit/bioedit.html]
  - Latest version: BioEdit_7.09_20070627.zip (runs on Windows Vista)
  - Older Version: BioEdit 7.0.1 updated 8/14/2004 (BioEdit_701_081704.zip)
  - NOTE: "BioEdit is not currently available for download.
    When the author can find time to upgrade it to a more stable and reliable version, it will again be made available for free download. Thank you for your understanding."
- jalview for Windows [a Java multiple alignment editor - release 2.2.1 - Feb 12, 2007]- (jalview_win_install_2.2.1_20070212.exe, without JRE) - Jalview is a multiple alignment editor written in java. You will need to install the java run time environment (JRE) available in the general purpose software links (above). It is used widely in a variety of web pages (e.g. the EBI clustalw server and the PFAM protein domain database) but is available as a general purpose alignment editor. http://www.jalview.org/
Phylogenetic Analysis
- Phylip PHYLIP 3.66 (Aug 4, 2006) - free package of programs for inferring phylogenies. http://evolution.genetics.washington.edu/phylip.html
  - For Intel-compatible processors with Windows95, Windows98, WindowsNT, Windows 2000, Windows me, or Windows XP download all of these:
  - Documentation and C source code - phylipw_3_66.exe
  - Windows95/98/NT/2000/me/xp executables, part 1 - phylipwx_3_66.exe
  - Windows95/98/NT/2000/me/xp executables, part 2 - phylipwy_3_66.exe
- Phylip on the Web - http://evolution.genetics.washington.edu/phylip/phylipweb.html
- PAUP -
- MEGA (Molecular Evolution Genetic Analysis) -MEGA 4.0 for Windows (Jul-03-2007) - MEGA4_Setup.zip http://www.megasoftware.net/ - MEGA is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses include sequence data alignment and assembly features.
  Previous version: MEGA 3.1 for Windows (MEGA31Setup.zip)
- PAML - Phylogenetic Analysis by Maximum Likelihood - package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Website: http://abacus.gene.ucl.ac.uk/software/paml.html - only available for command-line
- GARLI - Genetic Algorithm for Rapid Likelihood Inference - http://www.bio.utexas.edu/faculty/antisense/garli/Garli.html
- MrBayes - Bayesian Inference of Phylogeny - http://mrbayes.csit.fsu.edu/
- TreeView - TreeView is a simple program for displaying phylogenies. treev32.zip (version 1.6.6 - from Sep 3, 2001) - http://taxonomy.zoology.gla.ac.uk/rod/treeview.html (problem with website)
- NJplot (njplotWin95.exe / 24-Jul2006) is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. http://pbil.univ-lyon1.fr/software/njplot.html
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Epitope Prediction:
- IEDB Analysis Resource - includes epitope prediction -Web: http://tools.immuneepitope.org/tools/jsp/menu.jsp
- Antigenic (part of Emboss) - finds antigenic sites in proteins - Web: http://bioweb.pasteur.fr/seqanal/interfaces/antigenic.html
- Conformational Epitope Prediction Server -Web: http://202.41.70.74:8080/cgi-bin/cep.pl
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Protein Structure Viewers
- CD-Tree 3.0 with preview release of Cn3D 4.2 for Windows (CDTreeSetup3_0.exe) - CDTree is a protein domain hierarchy viewer and editor. Cn3D is a helper application for your web browser that simultaneously displays structure, sequence, and alignment, and has powerful annotation and multiple alignment editing features. http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml
- DeepViewer/Swiss-Pdb Viewer (latest: spdb37sp5.exe - version 3.7 service pack 5, released June 6, 2003): Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. http://swissmodel.expasy.org/spdbv/
Modelling
- MODELLER ver 9v1 (22Jan2007) is used for homology or comparative modeling of protein three-dimensional structures . available free of charge to academic non-profit institutions. Website: http://salilab.org/modeller/
- MODELTEST (modeltest3.7.zip / 23-Jun2005): A tool to select the best-fit model of nucleotide substitution. Website: http://darwin.uvigo.es/software/modeltest.html
  - FindModel - web implementation of MODESLTEST - http://hcv.lanl.gov/content/hcv-db/findmodel/findmodel.html
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Bioinformatics Utilities
- Biogrep (biogrep-1.0.tar.gz): Biogrep is a tool designed to quickly match large sets of patterns against biosequence databases Website: http://web.mit.edu/bamel/biogrep.shtml
- Sequence Manipulation Suite (sms2.zip) : is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing. Website: http://www.bioinformatics.org/sms2/
- Readseq 2.1.24: (readseq.jar 24May2006) Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences. Requires Java.
  - Run: java -jar readseq.jar
  - Web: http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi
  - Web: http://www-bimas.cit.nih.gov/molbio/readseq/ (many web version available)
- PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input. Website: http://www-unix.mcs.anl.gov/compbio/PatScan/
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~~SeqVista -A Graphical Tool for Sequence Feature Visualization and Comparison (latest version 1.81 Aug 3, 2005) - SeqVISTA_1.81_win.zip - http://zlab.bu.edu/SeqVISTA/~~
R Statistical Package (R-2.4.0-win32.exe) [27.94 MB] - R version 2.4.0 released on Oct 3, 2006 - R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. http://www.r-project.org/
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Last updated: Saturday, August 11, 2007 10:53 (EDT Time Washington DC)