Resource Access

Resource access is provided through our PORTAL site (authentication required). From this site you will be able to launch analyses through a easy web interface or open a VNC session (X-windows simulation) on the computing cluster.

If you are not registered yet please go through our User Registration page.

These are the applications presently implemented:

• BLAST (Basic Local Alignment Search Tool) is the heuristic search algorithm employed by the programs blastp, blastn, blastx, tblastn, and tblastx; these programs ascribe significance to their findings using the statistical methods of Karlin and Altschul with a few enhancements. The BLAST programs were tailored for sequence similarity searching - for example to identify homologs to a query sequence. The programs are not generally useful for motif-style searching, or for searching with short sequences.
• Nucleic acid sequence databases and analysis utilities:
  • FETCH - Fetch sequences from the databases embl, genbank, swissprot, pir, nrl3d, trembl
  • EMBOSS - European Molecular Biology Open Software Suite (with JEMBOSS interface)
  • STADEN - The Staden Package is a software package to perform most aspects of large scale sequence analysis. It including DNA sequence assembly tools, sequence analysis, sequence comparison and library handling/searching. It attempts to automate the process as much as possible without sacrificing the possibility of human intervention for quality control.
• Utilities for analysing and predicting the structure of RNA:
  • VIENNA - Vienna package for RNA structure analysis, used for predicting minimum free energy secondary structures, calculating the partition function for the ensemble of structures, calculating suboptimal structures in given energy range, predicting melting curves, searching for sequences folding into a given structure, comparing secondary structures including pairwise alignment.
• Utilities for editing and reformatting sequences:
  • CLUSTALX - 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.
  • SEAVIEW- A multiple sequence alignment editor
• Utilties for phylogenetic analysis:
  • PHYLIP - It is a package of programs written by Joe Felsenstein for phylogenetic analysis
  • PUZZLE - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can also be calculated under the clock-assumption. In addition, TREE-PUZZLE offers likelihood mapping, a method to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio to test the clock hypothesis, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids, and F81 for two-state data. Rate heterogeneity is modelled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set.
  • MRBAYES - MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods. MrBayes has a console interface and uses a modified NEXUS format for data and batch files. It handles a wide range of probabilistic models for the evolution of nucleotide and aminoacid sequences, restriction sites, and standard binary data. The user can set the priors used for the parameters and search for trees under topological constraints. The behavior of the Markov chain can be controlled by setting proposal probabilities for different move types and by invoking heated chains (Metropolis Coupling) to improve performance for difficult problems. Various options are available for summarizing the posterior distribution of the model parameters, including topology and branch lengths, and drawing inferences about ancestral states and site rates.
• Utilities for constructing physical genomic maps:
  • CRIMAP - The main purpose of Crimap is to allow rapid, largely automated construction of multilocus linkage maps (and facilitate the attendant tasks of assessing support relative to alternative locus orders, generating LOD tables, and detecting errors). Although originally designed to handle codominant loci (eg. RFLPs) scored on pedigrees "without missing individuals", such as CEPH or nuclear families, it can now (with some caveats) be used on general pedigrees, and some disease loci.
• Programs to map genes using pedigree and population data:
  • GLUE - It is a web-based interface to linkage and statistical genetics programs. It simplifies the use of commonly used programs through graphical selection of program options, automation of multiple analyses, and uploading of local files to the RFCGR file space.
  • FASTLINK - 'Fastlink' versions of the original LINKAGE package
  • VITESSE - Rapid Multipoint Likelihood Calculation
  • APM - Affected Pedigree Member method programs
  • SIMWALK2 - Multipoint analyses using simulated annealing
  • SPLINK - Linkage analysis using affected sib pairs
  • SIMIBD - Statistics of shared markers of affected relatives
  • GENEHUNTER - Multipoint analysis of pedigree data
  • MERLIN - Multipoint Engine for Rapid Likelihood Inference
  • TRANSMIT - Tests association of marker and disease
  • UNPHASED - Association and TDT for haplotypes
  • GENEHUNTER-PLUS - Modification of genehunter
  • SNPHAP - Haplotype frequency estimation
  • QUIKLINK - Alternative to LCP
  • MEGA2 - Linkage file format conversion utility