Welcome to Sequedex’s documentation!

• 1. Copyright notice
• 2. Introduction to Sequedex
  • 2.1. What is Sequedex?
  • 2.2. What does Sequedex do?
  • 2.3. How is Sequedex different from other sequence analysis packages?
  • 2.4. Who uses Sequedex?
  • 2.5. How is Sequedex used with other software?
  • 2.6. How does Sequedex work?
  • 2.7. Sequedex’s outputs
• 3. Installation instructions
  • 3.1. System requirements
  • 3.2. Downloading and unpacking for Mac
  • 3.3. Downloading and unpacking for Linux
  • 3.4. Downloading and unpacking for Windows 7 or 8
  • 3.5. Using Sequedex with Cygwin installed under Windows
  • 3.6. Installation and updates without network access
  • 3.7. Testing your installation
  • 3.8. Running Sequedex on an example data file
  • 3.9. Obtaining a node-locked license file
  • 3.10. Installing new data modules and upgrading Sequedex - User-installs
  • 3.11. Installing new data modules and upgrading Sequedex - System-installs
• 4. Getting started
  • 4.1. Running Sequescan
  • 4.2. Output files - stats
  • 4.3. Graphical output: Sequinator
  • 4.4. Output files - Who?
  • 4.5. Output files - What?
  • 4.6. Output files - Who does what?
  • 4.7. Obtaining annotated reads: Analysis of E. coli proteome
  • 4.8. Analysis of multiple files in parallel with the GUI
  • 4.9. The virus1252 data module
  • 4.10. Alternative data modules and memory usage
  • 4.11. Running Sequedex from the command line
  • 4.12. The Sequedex configuration utility and sequescan.conf
  • 4.13. Directory structures for data, output files, and analysis
• 5. Initial analysis with Sequedex: Phylogenetic and functional profiles
  • 5.1. Acquiring data files
  • 5.2. Phylogenetic rollups
  • 5.3. Functional rollups
  • 5.4. Normalized functional profiles
• 6. Using Sequestat
  • 6.1. Visualizing phylogenetic data with Sequestat
  • 6.2. Reading Life2550 output files into Sequestat:
  • 6.3. Reading virus1252 output files into Sequestat:
  • 6.4. Decomposing mixture into components with Sequestat
• 7. Functional analysis
  • 7.1. Visualizing SEED functional profiles with Sequestat
  • 7.2. Top 100 functional categories
  • 7.3. Identifying enriched functions
  • 7.4. Visualizing distribution of functions
  • 7.5. Profiling Chlorella kinases
• 8. Comparing Samples
  • 8.1. Scalar product of profiles
  • 8.2. Principal component analysis
  • 8.3. Ploting significant differences between two profiles
  • 8.4. ANalysis Of VAriance
  • 8.5. Clustering multiple profiles with R
  • 8.6. Visualizing the clusters with R
  • 8.7. Niche determinants, gulf oil
• 9. Annotated reads
  • 9.1. Obtaining annotated reads
  • 9.2. Phylogenetic filtering and assemblies of genomes
  • 9.3. Functional filtering
  • 9.4. Translated reads
  • 9.5. Gene-specific BLAST databases
  • 9.6. Placing reads into a multiple sequence alignment: conserved part of RNAP
  • 9.7. Obtaining specific genes
  • 9.8. Targeted assemblies of genes
  • 9.9. Nucleotide alignments
  • 9.10. Obtaining ribosomal (and tRNA) reads
  • 9.11. Aligning to a reference genome
• 10. Reference
  • 10.1. Command line options for sequescan
  • 10.2. Environmental variables
  • 10.3. Configuration options
• 11. Additional software tools and resources for use in conjunction with Sequedex
  • 11.1. Graphing and sorting with Excel
  • 11.2. How to install Cygwin and what to include.
  • 11.3. The command line with standard tools (Linux, Mac, Cygwin for Windows)
  • 11.4. Exploring trees with Archaeoptrix, FigTree, or NJPlot
  • 11.5. Comparing and annotating phylogenetic and functional profiles with Gnuplot
  • 11.6. Statistical analysis and graphing with R and R Studio
  • 11.7. Obtaining reference data from NCBI
  • 11.8. Creating synthetic data
  • 11.9. Comparing functional profiles to KEGG
  • 11.10. The Ribosomal Database Project
  • 11.11. Bergey’s manual
  • 11.12. Phylogeny vs. taxononomy - MEGAN and Krona plots
  • 11.13. Removal of duplicate reads with CD-HIT
  • 11.14. BioPython, BioPerl, and EMBOSS utilities
  • 11.15. BioEdit and reference alignments
  • 11.16. BLAST and nr / nt databases
  • 11.17. HMMER and Pfam
  • 11.18. Muscle
  • 11.19. Velvet and de-novo assembly
  • 11.20. Tree building with phyML or FastTree
  • 11.21. p-values and Pplacer
  • 11.22. BWA and BowTie2
  • 11.23. Samtools and Bamtools
  • 11.24. The Integrated Genomics Viewer
• 12. Tree of Life, 2550 taxa
  • 12.1. Bacteroidetes, et al.
  • 12.2. Alpha proteobacteria, et al.
  • 12.3. Beta and Gamma Proteobacteria
  • 12.4. Actinobacteria
  • 12.5. Firmicutes, et al.
  • 12.6. Cyanobacteria
  • 12.7. Archaea
  • 12.8. Eukaryotes
• 13. Definition of functional classifications
  • 13.1. Amino Acids and Derivatives
  • 13.2. Carbohydrates
  • 13.3. Cell Division and Cell Cycle
  • 13.4. Cell Wall and Capsule
  • 13.5. Clustering-based subsystems
  • 13.6. Cofactors, Vitamins, Prosthetic Groups, Pigments
  • 13.7. DNA Metabolism
  • 13.8. Dormancy and Sporulation
  • 13.9. Fatty Acids, Lipids, and Isoprenoids
  • 13.10. Iron acquisition and metabolism
  • 13.11. Membrane Transport
  • 13.12. Metabolism of Aromatic Compounds
  • 13.13. Miscellaneous
  • 13.14. Motility and Chemotaxis
  • 13.15. Nitrogen Metabolism
  • 13.16. Nucleosides and Nucleotides
  • 13.17. Phages, Prophages, Transposable elements, Plasmids
  • 13.18. Phosphorous Metabolism
  • 13.19. Photosynthesis
  • 13.20. Potassium metabolism
  • 13.21. Protein Metabolism
  • 13.22. RNA Metabolism
  • 13.23. Regulation and Cell signaling
  • 13.24. Respiration
  • 13.25. Secondary Metabolism
  • 13.26. Stress Response
  • 13.27. Sulfur Metabolism
  • 13.28. Virulence, Disease, and Defense
  • 13.29. Ribosome
  • 13.30. 0963 No Function Match
• 14. Viral tree, 1252 taxa
  • 14.1. dsDNA viruses 1: Baculoviridae, Phycodnaviridae, and Irdoviridae
  • 14.2. dsDNA viruses 2: Papillomaviridae and Polyomaviridae, and Poxviridae
  • 14.3. dsDNA viruses 3: Adenoviridae and Herpesviridae
  • 14.4. Reverse transcriptase viruses: Caulimoviridae, Retroviridae, and Hepadnaviridae
  • 14.5. ssRNA+ 1: Caliciviridae, Nidovirales
  • 14.6. ssRNA+ 2: Flaviviridae
  • 14.7. ssRNA+ 3: Tombusviridae and Virgaviridae
  • 14.8. ssRNA+ 4: Tymoviridae
  • 14.9. ssRNA+ 5: Picornaviridae, Togaviridae
  • 14.10. ssRNA+ 6: Potyviridae
  • 14.11. ssRNA, segmented: Arenaviridae, Bunyaviridae
  • 14.12. Mononegavirales
  • 14.13. Orthomyxoviridae
  • 14.14. ssDNA 1: Parvoviridae
  • 14.15. ssDNA 2: Geminiviridae_1
  • 14.16. ssDNA 2: Geminiviridae_2
  • 14.17. dsDNA: Reoviridae
• 15. Reference data
  • 15.1. Phylogenetic placement of RNA Polymerase reads
  • 15.2. Nucleotide Alignments for Strain Attribution