cluster_label

bioservx/bioserv2

 

Server 1: bioservx (head)

  • Intel Xeon Quad Core 5335 (2GHz x 2; 8GB; 80Gx2 +750Gx4; CentOS 5)
  • Slave nodes: node01 - node18
    (Intel Xeon or AMD Quad Core; 2.0 - 2.93GHz x 2; 8 - 16GB)

Server 2: bioserv2 (node3)

  • Dell Precision Workstation MT530 (1.7GHz x 2; 2GB; 34G+230Gx2; CentOS 4.5)
  • Slave nodes: node6 - node12
    (MT530/MT650N; 2.2 - 2.8GHz x 2; 2 - 4GB; Red Hat 9.0 or CentOS)

General User Guideline <<< Please read this!!


Portable Batch System — Load management system used on our servers


Databases available on our servers

 

Note: Information below has not been updated

BAliBASE: A benchmark alignment database

GPCRDB: Information system for G protein-coupled receptors (GPCRs)

NCBI databases

  • Main database files:
    • Unformatted: FASTA format w/ annotations (directory: /home/data/databases/blast/db/UnformattedDB)
    • Formatted: Used for BLAST search (directory: /home/data/databases/blast/db/OurFormattedDB)
  • Update: weekly (and monthly full download from NCBI)
  • NCBI Blast web page
  • Associated program: BLAST (see Software section below)
  • Database lists:

Pfam: Database of protein domains and HMMs

PRINTS: Protein Fingerprint Database

PROSITE: Database of protein families and domains

SWISS-PROT: Protein Knowledgebase
TrEMBL: Computer-annotated supplement to SWISS-PROT


Software available on our servers

 

Note: Information below has not been updated

BLAST: Basic Local Alignment Search Tool (homology search tool)

ClustalX and ClustalW: Multiple sequence alignment program

  • Version: 1.82 (directory: /usr/export/clustalx1.82.linux)
  • Commands:
    • clustalx (X-Window version)
    • clustalw (Command-line version)
    • clustalw1.81 (The old version. See NOTE below)
  • Manual: clustalx 1.81 manual
  • Manual: clustalw 1.8 (1.7) manual
  • Download from: ftp://ftp.ebi.ac.uk/pub/software/
    [available also for DOS/Windows, Mac, Mac OS X]
  • NOTE: "Clustalw1.82" has a problem with its command line execution. The older version, "Clustalw1.81" doesn't seem to have this problem. The menu execution of either version does not seem to be affected.

EMBOSS: The European Molecular Biology Open Software Suite

  • Version: 2.5.1 (directory: /usr/export/EMBOSS-2.5.1)
  • Commands: [currently available from Staden Package, see below]
  • Information: EMBOSS home page

Entrez: A search and retrieval system for NCBI databases

  • Commands:
    • entrez, entrez2 (X-Window version)
    • entrcmd (Command-line version)
  • Information: Entrez Help Document
  • NOTE: For entrcmd, just type entrcmd to see the list of options

HMMER: Profile hidden Markov models for biological sequence analysis

  • Version: 2.2g (directory: /usr/export/hmmer-2.2g.bin.intel-linux)
  • Information: HMMER home page

ITERALIGN - A program for the multiple alignment of protein sequences

MetaPIGA: Phylogeny Inference using the MetaGA

MODELTEST

MrBayes: Bayesian inference of phylogeny

MultAlin: Multiple sequence alignment by Florence Corpet

MULTICLUSTAL: A Perl script to automatically improve ClustalW

  • Version: 1.1 (directory: /usr/export/MULTICLUSTAL)
  • Command: MULTICLUSTAL.sh or MC.pl
  • Bioinformatics paper
  • Perl scripts: MC.pl & MC2.pl (requires also clustalw and boxshade to run it)
  • NOTE1: The Perl script above is modified, so it now uses the correct tree file from clustalw. Read the comment in the script.
  • NOTE2: The clustalw1.82 has a problem with the command line execution. In order to run Multiclustal, the older version, clustalw1.81 needs to be used.
  • NOTE3: The original MC.pl script supports only protein scoring matrices. In order to use Multiclustal for DNA alingments as well, use MC2.pl. It takes two options:
       -deep: for detailed analysis (with smaller steps). This can be used also with the original MC.pl script.
       -nuc: a new option to use DNA specific matrices and gap penalties.

Multiple Alignment Editors (for manual as well as ClustalW alignments)

PAUP: Phylogenetic Analysis Using Parsimony

  • Version: PAUP*4.0b10: Portable version for Unix/Linux (directory: /usr/export/paup)
  • Command: paup
  • Information: PAUP home page
  • Macintosh (Classic) version is also available on our lab Macintosh

PhyBayes: A program for Bayesian inference in phylogenetics

  • Version: 0.2e (directory: /usr/export/PhyBayes)
  • Command: phybayes
  • Information: PhyBayes page by Stéphane Aris-Brosou
  • Note: Copy 'mcmctree.ctl' file from '/usr/export/PhyBayes' directory into your working directory. Two data file names (sequence and tree files) need to be given in the 'mcmctree.ctl'.

Phylip: the PHYLogeny Inference Package

r8s: Analysis of rates (r8s) of evolution (and other stuff)

SAM: Sequence Alignment and Modeling

Staden Package [including the GUI to EMBOSS]

  • Version: 2002.0 (directory: /usr/export/staden-linux-2002.0)
  • Command: spin, pregap4, gap4 (X-Window required)
  • More information: Staden Package home page

S-PLUS: A Statistical Package

  • Version: 6.1 Release 2 for Linux
  • Commands:
    • to start the command-line mode without Java: Splus
    • to start the command-line mode supporting Java graphics (X-Window required): Splus -j
    • to start the S-PLUS graphical user interface (X-Window required): Splus -g &
  • MASS Library (version 4.0: MASS, nnet, class, spatial) are located in /usr/local/lib/VR7

SVM-light: Support Vector Machine

T-COFFEE: Multiple Sequence Alignment Package




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