Genomics Software offered by the BCF

Software for Windows and Macintosh computers:

• DNAStar LaserGene - for installation help go here.

• Vector NTI - for installation help, site licensing and software: Windows, Macintosh.

• Oligo - for installation help go here.

Server-based Software:

Quickindex: (follow link to find status; some programs may require some setup; contact Bo Demeler or Steve Hardies for additional help).

1. Local NCBI Blast Suite Implementation
2. EMBoss
3. Consed
4. Phred
5. Phrap
6. Accelrys GCG
7. HMMER
8. Phylip
9. Topo
10. MSE
11. SAM
12. Clustal W
13. SeaView
14. T_coffee
15. Stride
16. ReadSeq
17. PAUP
18. CLUMP
19. GeneHunter
20. Base-by-Base (BBB)
21. PEDSYS
22. Treeview

Note: use of these programs requires a Unix shell account. If you don't have an account you can apply for one here

• BLAST - a local implementation of the NCBI Blast Suite, including local daily updated copies of NCBI's protein and nucleotide databases, the Blast family, Psi-Blast, RPS-Blast, BlastClust, Regular expression searching, Impala, and utilities for extraction of sequences from local databases and construction of PSSMs. The programs are offered through two interfaces: 1) a web interface on the bioinformatics server, or 2) from a unix shell account. The latter requires no graphics interface and contains additional functionality over the web interface. See the following local help file for specific functional differences of searching at NCBI, at the local web interface, or from a unix shell. Referencing the local databases by GCG or other programs is also described.
  • Status:
    • (11-1-5)Rpsblast database (/ncbi/rps-blast) updated. Only on bcf.
    • (11/30/4) Netblast updated to version 2.2.10.
    • (7/2/4) Rpsblast database (/ncbi/rps-blast) updated to version 5/11/04.
    • env.nt and env.nr (DNA and translated sequence derived from environment (ie. a mixture from multiple organisms) databases added to nightly updated blast searchable databases.
    • (6/4/4) NCBI Toolkit has been upgraded to version 2.2.9. Due to update to Version 9.1 of Linux Slackware, old version (/usr/local/blast.old and /usr/local/blast.old.old) fails with Segmentation Faults, unless .ncbirc is in the default directory. Thus far version 2.2.9 appears to be working transparently.
    • The latest "month" database are no longer supported. Instead one can use the "limit to Entrez query" option to limit a search to entries from any arbitrary time interval.
    • Obsolete database document from NetBlast page has been replaced.
    • Search with Entrez query for NetBlast has been repaired.
    • Problems recently experienced with Nucleotide databases est and nr have been repaired.
    • Standalone blastpgp giving "segmentation error" when searched against joint databases (ie, -d "$BLAST_DB/nr my_database"). This is traced to a bug in the most recent release of the package from NCBI. You can work around this problem by substituting the older version by running the command as /usr/local/blast.old/blastpgp. Note: Old version fail with Segmentation faults unless .ncbirc is in default directory.
    • The database previously called "htg" is now called "htgs".
    • Otherwise, all functions tested and working as advertised except RPS-blast from the NetBlast interface is running very slowly. Turnaround time from the local Blast programs is about 5 times faster than from NCBI. RPS-Blast from the unix shell is about as fast as from the NCBI CDD search site.

• EMBOSS is a new, free Open Source software analysis package specially developed 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. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS modules can be accessed with the jemboss JAVA interface or by typing "emnu" at the command line. Notable capabilities include sequence alignment, searching, and analysis of all kinds, and support for enzyme kinetics.
  • Status:
    • 5-23-6: version 3.0.0 installed.
    • This huge collection of programs is installed but not completely set up yet. The jemboss interface is not installed. If you want to try an Emboss program, you can use emnu to select a program to run from a text-based menu, or else run it by typing its name at the command line. Note also that tfm < program name > will give an online manual page for each program. The help documents at the EMBOSS Applications page often have sample input and sample output.
    • Databases: The only local sequence database set up for sequence retrieval in USA format, db:accession, is protein nr. nr:accession, or nr:gi-number will feed that sequence from the local blast-formatted database to any EMBOSS program. Sequences can be retrieved from nr by SwissProt identifiers (like aqp1_human), but the identifier has to be typed in all caps (nr:AQP1_HUMAN). The other databases are not set up for retrieval in this way yet, and programs that process multiple entries from a database are not set up yet. For other database sequence, you can retrieve the sequence as a fasta file either directly from NCBI Entrez, or by fastacmd -i accession -d $BLAST_DB/nr -o < fasta filename >, and just give the fasta filename in place of the db:accession syntax.
    • Graphics: Most EMBOSS graphics programs provide an option to either output to xwindows (meaning you have to have an X windows server on you machine to see the output), or to output to graphics files you can import and display locally. For output to the StarNet Xwin32 server (for PCs), you should set "pseudocolor" in the "other" tab of the configuration utility. For direct output to graphics files, we have only tested postcript. Depending on whether you want postscript in black and white or color, specify ps, or cps when prompted for graph type. Adobe distiller did not interpret EMBOSS postscript files well. Use Ghostview instead.
    • To get database access, you must have environment variable EMBOSSRC=/usr/share/EMBOSS. If you want automatic retrieval from remote databases, you can copy /usr/share/EMBOSS/.embossrc to your own space, modify it according to intructions in the links below, and set EMBOSSRC to the directory now holding your own configuration file.
    • Please contact Bo Demeler or Steve Hardies if you have interest in programs from this package.

  • Emboss home page
  • Administration guide

  • Quick guide.

• Phred/Phrap and Consed are the Washington University Sequencing Center's shotgun sequence assembly and contig display programs. They feature probabilistic interpretation of chromatograms for quality of data, automatic contig assembly with heuristic upweighting of high quality data, and automated recommendataion of primers for finishing. The philosophy of these programs is to remove human inspection from the sequencing process as much as possible and to allow residual human inspection to zero in on problem areas as efficiently as possible. The system has a substantial learning curve. But in testing versus more user-friendly options, we find that this system ultimately saves significant time and expense.

• Status:
• 5/22/2006 - Have upgraded to Consed15 and phred version: 0.020425.c. Phred now handles CEQ data. You will now need /share/apps/genome/bin in your Path. The phredpar.dat file is in /home/hardies/bin/PhredPar. It contains an entry for the ABI 310. "consed" is a psuedonym for consed_amd46_dyn. Phred, phredPhrap, addReads2Contig, and view_assembly have been tested. For the view assembly button, on small projects it will usually complain that all contigs have been excluded by user-selectable criteria. Dismiss that window, and look for another behind the main consed window, and decrease the number of reads and length of sequence required for view assembly to include the contig.
• Basic assembly with abi or Beckman CEQ data and consed have been extensively used by Steve Hardies, whom you should consult if you wish to use these programs at UTHSCSA [ e-mail (567-3735)]. Autofinish and Polyphred have not been used locally, and may therefore require some additional set up. Other functions should work, but have not been tested locally.
• Accessing Consed requires an X windows interface. The preferred method of access is through vncviewer.
• A local help file for setting up a Phred/Phrap project has been prepared. Instructions to find files in /home/user/hardies apply to bioinf, not bcf. For operation on bcf, you may need to scp those files from bioinf.
• Phred/Phrap/Consed Home Page

• Purpose of the vector.seq file (documentation)
• Accelrys GCG - Wisconsin Package was a comprehensive sequence analysis software package in its day, but is now somewhat outdated. It has a linux command line interface. An alternative graphics interface named seqlab is no longer implemented at UTHSCSA. Documentation can be obtained in Room 420D. Extensive online documentation is available through the GenHelp command.

  • Status:
  • 5/22/2006: GCG reinstalled on bcf after revision of op sys to ROCKs. The path to the startup script has changed to /share/apps/gcg/gcgstartup.ksh. See the help file.
  • summer 2005: GCG has been migrated to the new computer bcf. To run bcf, you should execute the command export LD_ASSUME_KERNEL=2.4.19 after initializing gcg. If you use a gcg initialization file as advised in the local help file, you should add this line to the end of that file. Note that the old obsolete GCG-formatted databases were not migrated to bcf.
  • The SeqWeb web interface to the UTHSCSA GCG implementation has been discontinued.
  • 4/21/2003 - GCG is back on-line after a temporary outage related to updating the license.
  • 4/21/2003 - The internal GCG databases are updated to the Feb., 2003 releases.
  • 1/27/2004 - The restriction enzyme database was updated. Note: you can always download a most recent copy from http://rebase.neb.com/rebase/rebase.html to your own directory and refer to it with -DAT= on the command line when running map or mapsort.
  • A local help file for GCG has been prepared.
  • The local databases internal to the GCG system are not frequently updated, and should not be used. See this document for how to cause the GCG blast and psiblast commands to refer to the local daily updated databases.
  • The experimental SRS function named "lookup" does not properly work.
  • The GCG PAUP functions are not implemented. Instead see the stand-alone PAUP implementation in this document.
  • For graphics output from command line functions, only .png format is supported. First run the command png.

• HMMER 2.3.2 is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. Basically, you give HMMER a multiple sequence alignment as input; it builds a statistical model called a "hidden Markov model" which you can then use as a query into a sequence database to find (and/or align) additional homologues of the sequence family.

  HMMER is Beowulf capable and can be run using the parallel virtual machine on 48 computing nodes simultanously. To start HMMER, enter the name of the desired binary at the bioinformatics server's command line. There are also manual pages for some of the binaries on the server. You can invoke the man pages by typing "man ". For example: man hmmconvert - will call up the hmmconvert man page.

  Status:
  • 6-9-6. You now must place /share/apps/hmmer in your PATH to access hmmer.
  • The most common use of HMMER is to search Pfam. If you just want to search a sequence through Pfam, there are extended facilities for doing that at the Sanger Center Pfam site. Also note that NCBI's RPS-Blast (aka CDD search) at NCBI or locally achieves a similar result much faster but with slightly less sensitivity for detecting divergent sequences.
  • There is a local help file for HMMER.
  • The parallel implementation mentioned above is not yet installed.
  • An up to date pfam library will be maintained at $HMMERDB. The version is revealed by echo $HMMERDB. See the release notes at the Pfam FTP site to tell if there is a more recent version. E-mail Steve Hardies or Jeremy Mann if you need a more recent version loaded.
  • $HMMERDB contains ascii and binary versions of Pfam_fs and Pfam_ls. The binary versions are named Pfam_fs.bin and Pfam_ls.bin. Either can be searched, but searching the binary version is much faster.
  • This hmmer implementation updates the GCG hmmer functions. GCG hummer can be redirected to search the up to date pfam library. See GenHelp.
  • HMMER Home Page

  • The HMMER User's Guide (PDF format)

• PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters.

  There is no global phylip command. A series of programs must be run in sequence to accomplish a particular tree build. Each program when run displays a text-based menu, which asks the users which options they want to set, and allows them to start the computation. The data are read into the program from a text file, which the user can prepare using any word processor or text editor (but it is important that this text file not be in the special format of that word processor -- it should instead be in "flat ASCII" or "Text Only" format). For programs that take sequence data as input, the sequences must be prealigned and in phylip format. The SeaView editor installed on bioinf can convert a variety of multiple alignment formats to phylip format. Most of the programs look for the data in a file called "infile" -- if they do not find this file they then ask the user to type in the file name of the data file.

  • Status:
  • Phylip version 3.6a3 direct from Phylip's home page. Version 3.6a3 is an alpha relase which means that you could encounter bugs in the programs themselves. However, there are important improved capabilities in version 3.6a3 over 3.5. The Phylip home page contains a list of upgrades to version 3.6a3.
  • Only drawtree and drawgram use a graphics interface, and then only if preview mode is selected. Drawgram worked wherever tested, although in some cases a double click or middle click was unexpectedly required to activate the menu buttons on the Xwin interface. To export Drawtree's display to StarNet's Xwin32, it was necessary to check "pseudocolor" in the "other" tab of Xwin32's configuration utility.
  • The path to the font files cited in the documentation is /usr/local/phylip-3.6a/ For example, you can answer the question requesting the font file with /usr/local/phylip-3.6a/font1
  • Online documentation for version 3.6a3.

• TOPO is a utility that draws an image of a transmembrane protein in a colored "beads-on-a-string" graphics format. Topo is implemented as part of the EMBOSS EMBASSY package. It can output to an Xwindows display or to a graphics file, hence a graphics connection is not strictly required. It can be accessed on the bioinformatics server by typing "topo" at the command line. "topo -h" shows more help. To get the best feeling for what this program does, view the sample output in the documenation link below.
  • Status:
    • For graphics output see comments for EMBOSS programs in general.
    • The test data corresponding to the help document would be specified as nr:AQP1_HUMAN in our system, not sw:aqp1_human. See comments about database access for EMBOSS programs in general.
  • TOPO Documentation

• MSE is a sequence editor for multiple biological sequences. The MSE interface is a lot like GCG lineup, but without the limitations on size or numbers of sequences. It can be executed from the command line by typing: "mse".
  • Status: MSE is an application from the EMBOSS EMBASSY package. Before attempting to run MSE give the command export TERM=vt200. A critical error in the documentation is that you have to issue the command "save" to save an altered alignment, not "exit". Also, the "edit" command does not appear to be implemented, and it is unclear if you can input anything other than an MSF alignment. SeaView can convert other alignment formats to MSF. Finally, "redraw", control-R, and control-W do not seem to completely redraw the screen after accessing the online help. You will be happier opening the copy of the help document below in a browser window.
  • MSE Help

• SAM (Sequence Alignment and Modeling System) is a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. SAM is much like HMMER, but has greater facilities for assembling very divergent superfamilies of protein sequence. Sam is also like running multiple rounds of Psi-Blast, but with intelligent treatment of gaps. If you currently use Psi-Blast to try to define domains, or to investigate family relationships, you should look into SAM.

  SAM includes programs and scripts for the SAM-T99 method of remote homology detection. SAM-T99 is an iterative HMM search method for creating an HMM from a single protein sequence or seed alignment using iterative search of a protein database. The method is currently the most sensitive purely-sequence-based remote homology detection algorithm. SAM-T99 is based on successful methods created for the CASP2 and CASP3 protein structure prediction experiments.

  The algorithms and methods used by SAM have been described in several pioneering papers from the University of California, Santa Cruz. These papers, as well as the SAM software suite, several servers, and links to related sites are available on the World-Wide Web.

  • Status
    • (6/8/6) SAM is currently out of service. Contact Steve Hardies if you need access to this program.
    • (6/4/4)Have upgraded to version 3.4. The local help guide still refers to version 3.1.1. Target99 referred in the local help guide still exists. There is now a target2k script described in the updated documentation from UC Santa Cruz. Other differences are that the model building scripts (fw0.5, etc.) described in the local help guide have been replaced by scripts with names w0.5, etc. There are utilities in version 3.4 beyond those in version 3.1.1 that have not been added to the local help guide yet (and we have not checked out). Version 3.1.1 still exists in /usr/local/sam3.1.1/bin, but most of the binaries now fail with segmentation faults after the Linux upgrade to Slackware version 9.1; so there is no point in using the old versions.
    • A copy of the UCSC documentation distributed with version 3.1.1 is on bioinf at /home/user/hardies/sam_doc1999.pdf, if needed to resolve confusion caused by the upgrade.
    • The local implementation,version3.1.1 was heavily tested. The basic target2k script of version 3.4 has been tested and appears to work very similarly to target99. New features to version 3.4 have not been locally tested.
    • For executing from the node array (other than node1=bioinf) the nightly updated nr library pointed to by $BLAST_DB should still available. However, for extensive parallel use, it is better to have the library mounted locally on each engaged node, as well as mounting the temporary scratch files locally. The node-local library /ncbi/schblast/nr is used for this purpose, but is not frequently updated. Ask Steve Hardies to do an update of schblast across the node array if you wish to use this library. Also preceed execution of target99 or target2k with export SAM_T99_CONF=/usr/local/sam/bin/samv2-t99.conf for target99, or export SAM_T2K_CONF=/usr/local/sam/bin/samv2-t2k.conf for target2k to cause the scratch directory to mount locally on each node in /tmp/sam.
    • The local SAM implementation does not require a graphics interface. Some elements of it produce .ps files, that you may have to process into your system through Adobe distiller or some comparable method. If you do access bioinf at the graphics desktop level, you can display the .ps files by just clicking on them.
    • A local help guide to the facilities of SAM has been prepared.
    • If you are interested in SAM, you should also explore the U.C. Santa Cruz SAM Server Site maintained by SAM's authors. The fold recognition library searched there is not implemented locally. The local implementation, by comparison, permits running various numbers of iterations, and starting from intermediate seed alignments.
    • A local target99 job starting with one sequence takes about 15 min. Starting with a large seed alignment, it may take 4-8 hours.
  • SAM Documentation
  • ISMB99 Tutorial - Making the most of your hidden Markov models

• Clustal W Clustal W is the premier method for multiple alignment of divergent sequences. It uses progressive alignment, which means that closer sequences are aligned first, and prealigned sequences are represented by profiles during alignment. The implementation has a variety of alternatives for improving gap placement guided by secondary structure or arbitrary user intervention. Clustal is found in some form in many other packages (eg. GCG pileup), or at various web servers, although often restricted in some way. The bioinf implementation is release 1.82. Look to this implementation to give the full range of options for overpowering difficult alignment problems. A graphics interface is not required. Run by typing clustalw. The interface is menu driven and each screen has context-specific help.

  • Status:The number of sequences handled by Clustal W depends on the amount of memory available in the executing computer. The bioinf implementation exceeds tolerances somewhere above 250x700 characters.
  • The SeaView alignment editor (see below) permits confining Clustal W to align a portion of a larger displayed alignment.
  • The clustal implementation within the site-licensed LaserGene package is advertised as being rewritten to accept arbitrarily large alignments. We haven't benchmarked it yet, but that would normally be expected to slow it down.
  • The current clustal W implementation includes the option to conduct NJ tree analysis with bootstrap support.
  • The following is a compilation of the ClustalW help files
  • A local help file is available.

• Seaview is a graphical multiple sequence alignment editor. SeaView is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTAL or t-Coffee programs to locally improve the alignment. It can be executed from the command line by typing: "seaview". It requires you to have a running X-windows display. To select a section for realignment, Select the sequence names with the mouse, select the region using the sites toolbar item, and then select align in the edit toolbar item.
  • Status: All components have been tested on both bioinf and bcf. 3/24/5 Updated to version 3/16/5. 3/24/5 Updated to version 3/16/5. 3/24/5 Updated to version 3/16/5. There is online documentation from the SeqView display window. To get the SeqView display on your screen, you will need at least 1024 x 728 pixels.
  • By default the "edit alignment" function will spawn a clustalw realignment of the selected block of sequence. It is possible to redirect the program to use t_coffee instead. For instructions see A help file prepared for t_coffee
  • Seaview Home Page
  • Seaview Help Page
  • Sample MASE format

• t_coffee is a multiple sequence alignment program that is an alternative to clustalw. It functions by calling clustalw and a variety of other fasta-like algorithms to create a library of opinions about the alignment. Then it seeks to find an optimal compromise among the different opinions. In this mode it is thought to be a few percent more accurate than clustalw. It however can perform advanced functions of incorporating information from other alignment sources (most notably structure alignments, but also including any alignment describing how a motif should be aligned), fusing different multiple alignments, or comparing and marking the discrepencies between two multiple alignments.
  • Status: 3/15/2005 Two versions are installed: 1.37 and 2.03. 2.03 is better at the standard clustalw-like alignment job, but it is a beta release that does not yet successfully perform some of the advanced functions. You get version 2.03 by default. Instructions for switching between version 2.03 and 1.37 are given in a help file prepared for the use of t_coffee. The help file also contains links to program documentation, a publication describing the program, and a remote web server that performs a variety of t_coffee functions.
  • As installed, a structure alignment would have to be made separately and supplied to t_coffee as an alignment file. The links to program SAP and fugue described in the documentation are not installed. These functions permit t_coffee to automatically incorporate structural alignment information if two or more of the sequences to be aligned are identified as entries in a structure database. You can access this functionality at the web server. The web server is also a good place to derive a pure structural alignment for use with the locally installed version.
  • The help file gives specific instructions for how to spawn t_coffee realignment from Seaview.
  • The associated program mocca, which aids in aligning repetitive domains within a sequence, is installed but we have not tested it. The t_coffee documentation linked within the help file gives some information for running mocca

• Stride: Knowledge - based protein secondary structure assignment from atomic coordinates. Generate secondary structure maps from a PDB structure file. Note: the program deduces secondary structure from the coordinates, not by reading the author's annotation. No graphics interface required. Type stride to get a summary of usage.
  • Status: Only the main function was tested on installation.
  • Stride Home Page
  • Stride Help Page

• ReadSeq: This is a relatively standard file conversion utility for a variety of formats of sequences, including multiple alignments. It requires an X-windows interface. Run by java -jar /usr/local/readseq/readseq.jar. Help can be obtained from a help menu within the program graphics interface. Non-graphic help files may be printed by java -cp /usr/local/readseq/readseq.jar help, and similar commands to access additional help files listed within that one.
• Status: The links from the graphics help menu are malfunctioning. Presumably that will be fixed soon. Readseq was only tested on one conversion: a clustalW multiple alignment file to a MSF format. It failed, apparently confused by the nature of the sequence labels that were derived by truncating the nr fasta headers. To be fair, clutalw formats are particularly known for program to program incompatibilities. We recommend using the SeaView editor as the file converter for formats it supports. Readseq supports a wide variety of odd formats, so it may be helpful to solve special conversion problems. However, due to our lack of experience with this program, the user is advised to check the conversion carefully.
• Readseq may be obtained also for PC implementation from http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
• PAUP: is a software package for inference of evolutionary trees, serving as a comprehensive introduction to phylogenetic analysis for beginning researchers, as well as an important reference for experts in the field. With the inclusion of maximum likelihood and distance methods in PAUP* 4.0, the new version represents a great improvement over its predecessors. In addition, the speed of the branch-and-bound algorithm has been enhanced and a number of new features have been added, from agreement subtrees to tests for combinability of data and permutation tests for nonrandomness of data structure.

  Besides having all the major phylogenetic reconstruction algorithms, PAUP has the feature that columns and/or rows from multiple alignments can be ommitted from the analysis without actually editing the multiple alignment. This is particularly useful for masking untrustworthy segments in alignments of highly divergent protein families. PAUP does not have alignment functions. Sequences must be previously aligned by some other mechanism. See ClustalW, SeaView, HMMER, or SAM. For use by PAUP, aligned sequences must first be converted to a nexus format. This can be done by SeaView. Alternatively, the PAUP tonexus command can be used to convert a variety of formats and write a nexus file. Commands to manipulate the data or carryout the phylogenetic analysis may be directly incorporated into the nexus file as an alternative to typing them at the PAUP interactive prompt. This allows saving back files that completely document how a complex tree construction was done.

  PAUP is started by typing paup in the command line on the bioinformatics server. A graphics interface is not needed. The interactive PAUP interface, signified by the "paup>" prompt stays in force until quit is typed. Data is loaded by execute file.nex. A copy of results printed to the screen is perserved using the log command.

  Status:

  • (5/26/6) Paup version paup4b10-x86-linux reinstalled.
  • (6/9/6) To use paup, you now need /share/apps/paup to be in your PATH.
  • The online help only lists the available commands. The major commands, like log and quit are in a separate block that tends to roll off the screen and hide. Much of the functionality is in options not listed in the online help. Referring to the documentation linked below is essential. A new user should first work through the tutorial in the Quick Start Guide linked below. The version of PAUP implemented on bioinf is the one labeled "portable" in the Quick Start guide. The sample data cited in the Quick Start guide can be found in /home/hardies/bin/paupdir.
  • Users should generally open a log file immediately and keep it open until they want to quit. Otherwise, some lengthy calculations (notably bootstrap analysis) will dump their results to the screen in a way that is not subsequently retrievable.
  • Use the log function. Do not try to use Linux piped output.
  • The PAUP interactive interface does not always recover well if put into the background.
  • It is not necessary to run PAUP from the directory with the data as the Quick Start Guide suggests. Path names may be typed as part of filename specifications. However, environment variables do not expand at the paup prompt, so they can not be used to abbreviate path names.
  • The local PAUP has been extensively tested.
  • Quick Start Guide (PDF)
  • Command Reference (PDF)
  • PAUP Frequently Asked Questions
  • PAUP Home Page

• CLUMP: is a program designed to assess the significance of the departure of observed values in a contingency table from the expected values conditional on the marginal totals. The present implementation works on 2 x N tables and was designed for use in genetic case-control association studies, but the program should be useful for any 2 x N contingency table, especially where N is large and the table is sparse. The significance is assessed using a Monte Carlo approach, by performing repeated simulations to generate tables having the same marginal totals as the one under consideration, and counting the number of times that a chi-squared value associated with the real table is achieved by the randomly simulated data. This means that the significance levels assigned should be unbiased (with accuracy dependent on the number of simulations performed) and that no special account needs to be taken of continuity corrections or small expected values. The method is described in full in: Sham PC & Curtis D. 1995. Monte Carlo tests for associations between disease and alleles at highly polymorphic loci. Ann Hum Genet. 59: 97-105. Please cite this reference when using the CLUMP program.
  • CLUMP Documentation
  • CLUMP Sample Input File

    CLUMP syntax - execute on bioinf:

    clump Usage: clump infile outfile [tablefile]

• GeneHunter 2: is an extension of the GENEHUNTER software that provides the researcher with a much wider range of analyses for performing linkage and disequilibrium analyses. The backbone of the system is the same as GENEHUNTER - the very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size. This information is then used in exact computation of multipoint LOD scores, non-parametric linkage statistics, and now in a wide range of sibpair analyses (as in MAPMAKER/SIBS) and a new variance components analysis. In addition, several TDT analyses are also available for searching for association/disequlibrium in addition to linkage. As before, quick calculations involving dozens of markers, even in pedigrees with inbreeding and marriage loops, is possible with GENEHUNTER 2. Additionally, the multipoint inheritance information allows the reconstruction of maximum-likelihood haplotypes for all individuals in the pedigree and information content mapping which measures the fraction of the total inheritance information extracted from the marker data. All of these calculations are performed the same user-friendly environment as in GENEHUNTER.

  NB: This release (November 2, 1998) is the first Beta release of GENEHUNTER 2. As such, some features are not yet completed and others (such as the new 'variance components' and TDT functionality) will possibly be extended in the near future. It's been expressed that having the MAPMAKER/SIBS and TDT functionality in GENEHUNTER is sufficiently important that I am releasing this before everything that will eventually be in GENEHUNTER 2 is completed and fully tested. Thanks for your patience while we continue to develop the software. If there are features that you would like to see in upcoming versions - don't hesitate to write us or use the interactive web pages we're setting up (see 'SOFTWARE REGISTRATION' and 'Reporting Bugs or Errors' below).

  • GeneHunter online Help file (Put a copy of this file in your home directory on bioinf prior to starting genehunter)
  • Sample Marker Data File (linkloci.dat)
  • Sample Pedigree Data File (linkped.pre)
  • GeneHunter Documentation (Postscript format)
  • GeneHunter Documentation (PDF format)
  • GeneHunter Readme file

  To start GeneHunter, issue from the command line on bioinf:

  gh

• Base-by-Base (BBB) is a whole genome pairwise and multiple alignment editor. Base-By-Base hilights differences between pairs of alignments and allows the user to easily navigate large alignemts of similar sequences. Although Base-By-Base was intended as an editor and viewer for alignmets of highly similar sequences, it is also provides many of the functions of other generic alignment editors.
  • Base-by-Base is written in Java and can be access from the web at:

    http://www.virology.ca/pbr/bbb

    If users at UTHSCSA find that the response of this program is too slow, please contact Borries Demeler and we can install a local version of this software on our server.

• PEDSYS is a full-scale database system developed as a specialized tool for management of genetic, pedigree and demographic data.

  Pedsys is installed on the Bioinformatics Server and can be accessed from the command line by issueing the name of module prefixed by

  $PEDSYS/bin

  Example:

  $PEDSYS/bin/genefreq (Calculates gene and genotype frequencies from phenotypic data).

  For more information, please visit the PEDSYS Web site.

  A Manual in PDF Format is available from the local server.

• Treeview: A graphics program that displays tree files in any of the following formats: Nexus tree file, Nexus .nex file, TreeBase, McBayes consensus,clustal (.ph,.phb, .dnd), and Phylip. The "phylogram" display of the tree shows a scale bar if the tree file includes branch length information.
  • Installed on bcf only (4/13/5).
  • Run from desktop, or with X windows or vnc interface established by typing tv
  • The linux version installed lacks some functions (editing and unrooted trees) found in the version for MS-windows.
  • Treeview website.

Please let us know if you are interested in additional packages and we will help you get them installed. We can install and house Unix-based software packages for you.