MAGNet: Software

 
  • Editor's note: The MAGNet center formally closed in July 2016, following the mandatory conclusion of its grant after more than 10 years of activity. The pages in this section constitute an archive of its work.

Licensed software, fee based, available through HICCC

Application Company/Authors
Chromas Technelysium Pty Ltd
Feature Extraction Agilent
Flowjo -
LaserGene DNASTAR
Matlab Mathworks
Mutation Surveyor Softgenetics
Origin OriginLab
Sequencher GeneCode
SPSS SPSS

Licensed software available through HICCC

Application Source Description Location *
GCG-Wisconsin Package Accelrys - 2
BRLMM Analysis Tool Affymetrix - 2
GeneChip Targeted Genotype Analysis Affymetrix - 2
GeneChip Genotype Analysis Affymetrix - 2
GeneChip Data Transfer Tools Affymetrix - 2
GeneChip System Affymetrix - 2
Gene Copy Number Analysis Affymetrix - 2
Expression Console Affymetrix - 2
Tiling Analysis Affymetrix - 2
Genscan Burge and Karlin - 2
FlinchTV GeoSpiza - 2
VectorNTI Invitrogen - 2
NIS-Element Nikon - 2
Paracel Transcript Assembler Paracel Designed for large scale EST transcript reconstruction projects. Assembly is optimized specifically for the characteristics of EST datasets. Rigorous detection and alignment of alternative splice forms. Correct handling of chimeras and repeats. Handles deep assemblies where hundreds of ESTs overlap, including correct consensus base calling. Useful for coding region SNP analysis. 1
Paracel Genome Assembler Paracel Provides CAP4-based sequence assembly and multiple sequence alignment. Can be used for BAC, bacterial or viral genome sized projects. Provides for use of clone-pair constraints (paired end reads) in assembly. 1
Paracel Filtering Package Paracel Sequence filtering and masking. Sensitive repeat detection. (Includes the programs Scylla and Sequtil) 1
LightCycler Roche - 2

Location key: (1) C2B2, (2) HICCC.

Software available through C2B2/HICCC

Application Source Description Location *
Sequence
Molphy Adachi and Hasegawa   2
Phred/Phrap/Consed Higgens et al.    1, 2 
Rnabob Eddy   2
Rnamot Eddy   2
T-COFFEE   A Multiple Sequence Alignment Package. (C2B2 v 1.37).  Comparison with clustalw 1, 2 
JavaTreeview Saldhana   2
AAT Xiaogui Huang    2
BLAST/Seg/Dust NCBI   1, 2 
CustalX

Higgins et al.

 multiple sequence alignment and phylogenetic tree building (C2B2 v1.83)  1, 2 
ClustalW Higgins et al. multiple sequence alignment and phylogenetic tree building (C2B2 v1.83)  1, 2 
Fasta Pearson   2
BioPerl   Perl modules that provide many common bioinformatics tools for use in Perl scripts. 1
EMBOSS   a large package of sequence search and manipulation commands, similar to the GCG package 1
EMBOS EMNU   EMBOSS Menu is Not UNIX 1
EMBOSS MSE   v. 0.0.4 - A Multiple Sequence Screen Editor for Biological Sequences 1
EMBOSS TOPO   v. 0.1 - Transmembrane region "display"  1
fmtseq   part of the  seqio  package, fmtseq provides file format conversion between most popular formats including fasta, genbank, gcg, embl, phylip, clustalw and many others.  
HMMER 2.2g Sean Eddy  Programs for building HMMs. Please see the  User's Guide  (in PDF format). 1
MUMmer   a package of programs for comparing whole chromosomes or genomes in either nucleotide or protein sequence space. 1
SSAHA   Sequence Search and Alignment by Hashing Algorithm. "The SSAHA algorithm is most suitable for applications requiring exact or 'almost exact' matches between two sequences, such as SNP detection or sequence assembly." ( help file ). 1
Phylogeny
PAML   "Phylogenetic Analysis by Maximum Likelihood". Built as 64-bit binaries on the SUN V880 with access to the full 32 GB of RAM. 1
Phylip Adachi and Hasegawa The Phylogeny Inference Package (C2B2 v. 3.5c) 1, 2 
PAUP     1
Microarrary
The R Package   A language and environment for statistical computing and graphics. 1
SJava   A package that provides direct access to calling arbitrary Java methods and creating arbitrary Java objects from within R and also calling R functions from Java.  1
Bioconductor   An open source and open development software project to provide tools for the analysis and comprehension of genomic data (bioinformatics) 1, 2 
BRBArrayTools NCI   2
SAM Tibishirani et al.    2
Cluster 3.0  Eisen and deHoon    2
GenePattern MIT/Broad   2
ImaqQuant     2
Genetics
SOLAR   a suite of algorithms for linkage and quantitative genetic analysis: the Sequential Oligogenic Linkage Analysis Routines. From the Southwest Foundation for Biomedical Research. 1
Molecular Mechanics
X-PLOR   v. 3.851 - A System for X-ray Crystallography and NMR.  

Location key: (1) C2B2, (2) HICCC.

Notes

T-COFFEE is integrated into BioPerl. "T-COFFEE is more accurate than ClustalW for sequences with less than 30% identity, but it is slower...." (quoted from: http://www.ch.embnet.org/software/TCoffee.html)

PAML
By default, several of the PAML programs look for a control file (e.g. baseml.ctl) in your current directory. 

The codeml program (sometimes) makes use of data files that are provided with PAML. These files are available under: /projects/source/PAML/paml3.13

You need to give the full path to whatever PAML provided data file you are including in the codeml.ctl file. For instance: 

Documentation: Online documentation is available. In addition, the current PAML manual is available in pdf format. The online FAQ seems particularly useful.