Available Software

Software available at the terminal (SSH login)

In general, the computers in the grid should be used when you need more computer resources than what can be provided by your own desktop and/or laptop computer. It is also useful in those cases where you need to run a program which requires Linux.

Currently installed software is listed below, and we have created links to their homepages where you will find user manuals and usage instructions. We will not be posting instructions for each program here. Please feel free to update the usage descriptions if you feel they are outdated. (Just click the small pen in the title bar.)

Whenever you want to run jobs on the terminal, make sure to submit them through the queuing system. Otherwise they might be killed by the system after a relatively short run time. If your unsure how to do this, please contact Mykopat IT for help.

Assemblers and Related Software Abyss - ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. Blast2Go - Blast2GO is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. This service runs locally on our grid but uses a Java interface to link with the Blast2Go servers. Cap3 - The program has a capability to clip 5' and 3' low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward-reverse constraints to correct assembly errors and link contigs. Chimerachecker - a blast-based open source software package to examine newly generated fungal ITS sequences for the presence of potentially chimeric elements in batch mode. Mothur -Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.The package has accelerated versions of the popular DOTUR and SONS programs. Also included in the package is the functionality of a number of other popular tools including s-libshuff, TreeClimber? (i.e. the parsimony test), UniFrac?, distance calculation, visualization tools, a NAST-based aligner, and many other features.

• users can install and run this in their local folders. It can be downloaded from - here.

Oases - Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It is similar to Velvet, but optimised for transcriptome assembly. Tablet - Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. You can - search and locate reads by name or subsequence across entire data sets, do entire-contig overviews, showing data layout or coverage information and display of reads in both packed and stacked formats.

• users can install and run this in their local folders. It can be downloaded from - here.

Trinity - Trinity, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. The Trinity software package can be downloaded here. Velvet short read assembler - Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Can be used to do whole genome assemblies of Illumina Genome Analyzer (Solexa) data. InterproScan? - InterProScan? is a tool that scans given protein sequences against the protein signatures of the InterPro? member databases, currently--PROSITE, PRINTS, Pfam, ProDom? and SMART. The number of signature databases and their associated scanning tools as well as the further refinement procedures make the problem complex. InterProScan? is designed to be a scalable and extensible system with a robust internal architecture. Homology Searches and Alignment Blast/Blast?+ - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Blast + manual can be found here. Blat - is similar in many ways to Blast. The program rapidly scans for relatively short matches (hits), and extends these into high-scoring pairs (HSPs). However, Blat differs from Blast in some significant ways. Where Blast builds an index of the query sequence and then scans linearly through the database, Blat builds an index of the database and then scans linearly through the query sequence. Online Blat can be done here. Download Blat here. ClustalW - The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (​http://www.ebi.ac.uk/clustalw/). Exonerate - Is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Genewise - Predicts gene structure using similar protein sequences. The GeneWise? algorithm was developed from a principled combination of hidden Markov models (HMMs). Both algorithms are highly accurate and can provide both accurate and complete gene structures when used with the correct evidence. Download here. Mafft - is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc. Mosaik Assembler - MOSAIK is a reference-guided assembler comprising of four main modular programs: MosaikBuild?,MosaikAligner?, MosaikSort?, MosaikAssembler?. The manual can be download - here. Muscle - USearch - Gene Prediction/Annotation?

Maker - Repeat Maker - SamTools? -

Population Genetics

Mr Bayes -MrBayes? is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations.

• users can downloaded, compiled and install this in their local folders. It can be downloaded - here.

Mirgrate-n -Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters. It can be downloaded - here. Statistics Prrogams

R - R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R. To download R go - here. Programming Languages and Libaries Perl modules for BioPerl? - These are useful if you write your own perl scripts. Python modules for BioPython? - The Python ditto to BioPerl?.

All software we have compiled and installed ourselves is installed to the prefix $MYKOPAT_PREFIX, (e.g. ./configure --prefix=$MYKOPAT_PREFIX) and available on all machines with the same architecture. Please check the notes on the software page to see if it is also available on the Macs.

Remember you should leave the ./ out when you try to run a software. Even if the software manual say so.