Welcome to Sequedex’s documentation!¶
- 1. Copyright notice
- 2. Introduction to Sequedex
- 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
- 6. Using Sequestat
- 7. Functional analysis
- 8. Comparing Samples
- 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
- 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
- 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