Changes between Version 6 and Version 7 of Software


Ignore:
Timestamp:
Jul 5, 2011, 9:44:26 AM (13 years ago)
Author:
Patrik Söderström
Comment:

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  • Software

    v6 v7  
    55This list is under construction.
    66
    7  * MiraAssembler -
    8  * [wiki:Cap3Assembler] -
    9  * [wiki:Blast] - he 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.
    10  * [wiki: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
     7 * [wiki:MiraAssembler]
     8 * [wiki:Cap3Assembler]
     9 * [wiki:Blast]
     10 * [wiki:Blast2Go]
     11 * [wiki: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.
     12 * [wiki: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.
     13 * [wiki: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.
     14 * [wiki:Mosaik Assembler] - MOSAIK is a reference-guided assembler comprising of four main modular programs: MosaikBuild, MosaikAligner, MosaikSort, MosaikAssembler. The manual can be download - here.
     15 * [wiki: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.
     16 * [wiki: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
     17assembly. It is similar to Velvet, but optimised for transcriptome assembly.
     18* Perl modules for BioPerl - These are useful if you write your own perl scripts.
     19* Python modules for BioPython - The Python ditto to BioPerl.
     20* [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.
     21 * [wiki: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.