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Ab Initio Tutorial.pdf Download Firefox

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MessagePosté le: Sam 3 Sep - 22:14 (2016)    Sujet du message: Ab Initio Tutorial.pdf Download Firefox Répondre en citant

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Ab Initio Tutorial.pdf Download Firefox

Also appropriate for non-mailbox roles in a larger Exchange deployment. Need X11 support to run GUI Depends on java Depends on phyml KAAS - KEGG Automatic Annotation Server module name: KAAS version 2.0 Functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database To use: review instructions at /group/bioinfo/apps/apps/KAAS-2.0/readme.txt Then, copy /group/bioinfo/apps/apps/KAAS-2.0/kaas.config to your working directory Issue all KAAS commands from that directory Depends on ruby Depends on perl Depends on HMMER Depends on blast/2.2.26 khmer module name: khmer version 2012-07-06 In-memory k-mer counting Info in /group/bioinfo/apps/apps/khmer-2012-07-06/doc Forum: khmer is *pre-publication* and *research* software Depends on biopython/2.7.2 KmerGenie module name: kmergenie version 1.5692 Estimates the best k-mer length for de novo assembly Depends on R-bioconductor Depends on biopython/2.7.3 LRNAscaffolder module name: LRNAscaffolder version 14Feb2014 Long transcriptome reads to scaffold genome Manual: Depends on gcc Depends on perl/5.18.1 LAPACK Linear Algebra PACKage and BLAS module name: lapack version 3.4.2 compiled with gcc 4.7.2 Depends on gcc libgcrypt module name: libgcrypt version 1.5.3 General purpose cryptographic library Depends on libgpg-error libxml2 module name: libxml2 version 2.9.1 XML C parser and toolkit developed for the Gnome project Depends on gcc libxslt module name: libxslt version 1.1.28 XSLT C library developed for the GNOME project XSLT is a an XML language to define transformation for XML Depends on gcc Depends on libxml2 Lucy module name: lucy version 1.20p DNA sequence quality and vector trimming tool Manual: man lucy Depends on gcc lz4 module name: lz4 version 122 Extremely Fast Compression algorithm man lz4 Depends on gcc MACS module name: macs version 2.1.0 Other versions: 1.4.2a, 1.4.2b, 2.0.10, 2.0.10-2.7.2 Model-based Analysis for ChIP-Seq Info: /group/bioinfo/apps/apps/MACS-2.1.0/README.rst Depends on biopython/2.7.8 Depends on PeakSplitter MAFFT module name: mafft version 6.903 Multiple alignment program for amino acid or nucleotide sequences man pages for mafft and mafft-homologs MAKER module name: MAKER version 2.10 Other versions: 2.27b, 2.28b, 2.30p, 2.31.7 Genome annotation pipeline Info: Info: /group/bioinfo/apps/apps/MAKER-2.10/README Tutorial: Forum: Depends on perl Depends on SNAP Depends on RepeatMasker Depends on exonerate Depends on blast/2.2.26 Depends on AUGUSTUS Depends on GeneMark Depends on mpich2/1.4.1p1gcc-4.7.2 MAQ module name: maq version 0.7.1 MAQ: Mapping and Assembly with Qualities Manual: FAQ: Depends on gcc MaSuRCA (Maryland Super Read Cabog Assembler) module name: MaSuRCA version 2.1.0 Genome assembler Manual: /group/bioinfo/apps/apps/MaSuRCA-2.1.0/doc/MaSuRCAQuickStartGuide.txt Manual: /group/bioinfo/apps/apps/MaSuRCA-2.1.0/doc/MaSuRCAQuickStartGuide.pdf Need to copy /group/bioinfo/apps/apps/MaSuRCA-2.1.0/srconfigexample.txt into assembly directory and modify as needed Depends on gcc Depends on perl MATLAB Compiler Runtime (MCR) module name: MCR version 7.14 Shared libraries that enables the execution of compiled MATLAB applications Corresponds to MATLAB R2010b matrix2png module name: matrix2png version 1.2.2 Visualizations of microarray data and many other data types Manual at Examples at Depends on gcc Mauve module name: mauve version 2.3.1 Construct multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion Manual: Manual: /group/bioinfo/apps/apps/mauve2.3.1/mauveuserguide.pdf Note: Needs X11 support for GUI (not needed with command line utilities mauveAligner or progressiveMauve) Depends on java mcl module name: mcl version 12-068 The Markov Cluster Algorithm (MCL) MCL algorithm finds cluster structure in graphs man pages available Depends on gcc MeDUSA module name: medusa version 1.0 Pipeline for MeDIP-seq data analysis Info at /group/bioinfo/apps/apps/medusa-1.0/README Copy and change the config file in /group/bioinfo/apps/apps/medusa-1.0/configfiles/medusatemplate.cfg Depends on perl Depends on R-bioconductor Depends on bwa Depends on samtools Depends on fastqc Depends on USeq Depends on BEDTools MEGAN (MEtaGenome ANalyzer) module name: MEGAN version 5.2.3 Other versions: 4.70.4, 5.1.4 Software for analyzing metagenomes Release Notes: Need X11 support for program to run (ssh -X) Need license key from Depends on java MeQA module name: MeQA version 1.0.0 A pipeline for MeDIP-seq data quality assessment and analysis Need to copy /group/bioinfo/apps/apps/MeQA-1.0.0/example-config.cfg to your project dir and modify to suit your needs Depends on R-bioconductor Depends on biopython/2.7.2 Depends on bwa Depends on samtools Depends on BEDTools Depends on samstat Depends on CEAS MetaCV module name: metacv version 2.2.9 Composition based classification for short metagenomic sequences Manual: /group/bioinfo/apps/apps/metacv-2.2.9/MetaCVmanual.pdf Need to install prokaryotes database from website (>16GB compressed) Depends on gcc MetaVelvet module name: MetaVelvet version 1.2.01 A short read assember for metagenomics Built with MAX KMER LENGTH=99 and CATEGORIES=4 Depends on velvet METIS module name: metis version 5.0.2 Serial Graph Partitioning and Fill-reducing Matrix Ordering Manual: Manual: /group/bioinfo/apps/apps/metis-5.0.2/manual/manual.pdf Depends on gcc Microbiome Utilities Portal of the Broad Institute module name: microbiomeutil version r20110519 Provides microbiome utilities : - Sequence alignment (NAST-iEr) - Chimera detection (ChimeraSlayer, WigeoN) - Operational taxonomic unit OTU binning (TreeChopper) - Sequence assembly (AmosCmp16Spipeline) - database of reference 16S sequences Info: /group/bioinfo/apps/apps/microbiomeutil-r20110519/docs Depends on blast/2.2.26 Depends on cdbtools MicroRazerS module name: MicroRazerS version 1.0 Fast mapping short RNAs onto a reference genome Mailing list: Depends on gcc Minia module name: minia version 1.5418 Other versions: 1.5418-maxk128, maxk128, maxk32 Short-read assembler based on a de Bruijn graph Manual: /group/bioinfo/apps/apps/minia-1.5418/manual.pdf This version is compiled with support for maximum k-mer size of 32 Depends on gcc MIRA module name: mira version 4.0.2 Other versions:, 3.9.1, 3.9.10, 3.9.11, 3.9.12, 3.9.14, 3.9.15, 3.9.16, 3.9.18, 3.9.3, 3.9.4, 3.9.5, 3.9.7, 3.9.8, 3.9.9, 4.0, 4.0.1, 4.0rc1, 4.0rc2, 4.0rc3, 4.0rc4, 4.0rc5, 4.9.1, 4.9.3 Whole genome shotgun and EST sequence assembler Manual at Docs at /group/bioinfo/apps/apps/mira-4.0.2/docs Mailing lists: Depends on gcc Depends on tcl miRDeep module name: mirdeep version Discovering known and novel miRNAs from deep sequencing data Manual at Depends on perl Depends on bowtie Depends on ViennaRNA Depends on randfold miRDeep-P module name: miRDeep-P version 1.3 A computational tool for analyzing the microRNA transcriptome in plants Manual at Manual at /group/bioinfo/apps/apps/miRDP-1.3/miRDPmanual1.3.pdf Depends on perl Depends on bowtie Depends on ViennaRNA Depends on randfold MIREAP module name: mireap version 0.2 Reap miRNAs from deeply sequenced smRNA library Depends on perl Depends on ViennaRNA miRExpress module name: miRExpress version 2.1.3 Analyzing high-throughput sequencing data for profiling microRNA expression Usage: /group/bioinfo/apps/apps/miRExpress-2.1.3/README Includes data from miRBase 18.0 (2012APR27) Depends on gcc miRNAkey module name: miRNAkey version 1.2 A pipeline microRNA Deep Sequencing data analysis Manual: Need to copy /group/bioinfo/apps/apps/miRNAkey-1.2 to your project directory and run from there Depends on java Depends on bwa Depends on fastx Depends on perl MITObim module name: MITObim version 1.7 Other versions: 1.6 Mitochondrial baiting and iterative mapping Version 1.7 uses mira 4.0.x Info: /group/bioinfo/apps/apps/MITObim-1.7/ Test data: /group/bioinfo/apps/apps/MITObim-1.7/testdata1.tgz Depends on perl Depends on mira MOTHUR module name: mothur version 1.34.4 Other versions: 1.25.0, 1.25.1, 1.32.1 Microbial ecology tools mothur and uchime (not GUI version) wiki: forum: Depends on gcc MrBayes module name: mrbayes version 3.2.1 Bayesian Inference of Phylogeny Manual at Depends on beagle Mugsy module name: Mugsy version 1r2.3 Multiple whole genome alignment tool Depends on gcc Depends on muscle MUMmer module name: MUMmer version 3.23 Ultra-fast alignment of large-scale DNA and protein sequences Manual: Tutorial: Info: /group/bioinfo/apps/apps/MUMmer-3.23/docs Depends on gcc MUSCLE module name: muscle version 3.8.31 Other versions: 3.8.425 Multiple sequence alignment (faster than clustalw) Docs: MySQL Connector/J module name: mysql-connector-java version 5.1.21 Other versions: 5.0.5, 5.0.8 MySQL Connector/J is the official JDBC driver for MySQL Docs: /group/bioinfo/apps/apps/mysql-connector-java-5.1.21/docs Depends on java NCBI BLAST module name: blast version 2.2.30+ Other versions: 2.2.22, 2.2.25+, 2.2.26, 2.2.26+, 2.2.27+, 2.2.28+, 2.2.29+ Basic Local Alignment Search Tool Manuals: Release notes: Depends on gcc NCBI BLAST CGI programs module name: wwwblast version 2.2.26 BLAST CGI programs (legacy version) Docs: /group/bioinfo/apps/apps/wwwblast-2.2.26/docs This "legacy" version of NCBI BLAST is deprecated; see for reasons to use BLAST+ instead These are the wwwblast CGI programs. Licenses for each computer, rather than each user Adobe InDesign CC Desk Top Publishing Adobe InDesign (CC) for education Device licensing. Now available on Mac and Windows Autodesk DesktopPC Inventor Robot Structual Analysis Barcode font 3 of 9 Utilities A Font that format characters as Bar codes. in nEq. We need the latest version of the Ab Initio GDE help file. Disqus - Tl T5e1 7-pdf Split And Merge Download. It provides a balance of advanced analysis and point-and-click ease of use.

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