MykopatGrid? available software

This list is under construction.

• MiraAssembler?
• Cap3Assembler?
• Blast?
• Blast2Go?
• 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.
• 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.
• 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.
• Assembler? - MOSAIK is a reference-guided assembler comprising of four main modular programs: MosaikBuild?, MosaikAligner?, MosaikSort?, MosaikAssembler?. The manual can be download - here.
• 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.

• Perl modules for BioPerl? - These are useful if you write your own perl scripts.
• Python modules for BioPython? - The Python ditto to BioPerl?.
• [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.
  • 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.