Pandora's Toolbox for Bioinformatics
Pandora's Toolbox for Bioinformatics
About the Book
About the Author
Table of Contents
- 1. Introduction
- 2. List of programs
- 3. Rationale for inclusion
- 4. Server instructions
- 5. Programs
-
6. BLAST
- 6.1 Quick instructions
- 6.2 History
- 6.3 Further readings
- 7. BLAST tutorial
-
8. How BLAST works
- 8.1 BLAST score and E-value
- 8.2 Score
- 8.3 E-value
- 8.4 Core Algorithms
- 8.5 Rationale behind the Algorithm
- 8.6 Increasing the Speed of Smith-Waterman
- 8.7 Indexing
-
9. BWA-MEM
- 9.1 Quick instructions
- 9.2 History
- 9.3 Features
- 9.4 Further readings
- 10. BWA-MEM tutorial
-
11. How BWAMEM works
- 11.1 Details of algorithm
- 11.2 Details of code
-
12. FastTree
- 12.1 Quick instructions
- 12.2 History
- 12.3 Further readings
- 13. FastTree Tutorials
-
14. How FastTree works
- 14.1 Details of algorithm
- 14.2 Details of code
- 14.3 License
-
15. HMMER
- 15.1 Quick instructions
- 15.2 History
- 15.3 Further readings
- 16. HMMER tutorials
-
17. How HMMER works
- 17.1 Algorithm
-
18. Kallisto
- 18.1 Quick instructions
- 18.2 Features of Kallisto
- 18.3 Further readings
- 19. Kallisto Tutorial
-
20. How Kallisto Works
- 20.1 Algorithm
-
21. KMC
- 21.1 Quick instructions
- 21.2 Features
- 21.3 Further readings
- 22. KMC tutorial
-
23. How KMC works
- 23.1 Details of algorithm
- 23.2 Details of code
-
24. Minimap and Miniasm
- 24.1 Quick instructions
- 24.2 History
- 24.3 Further readings
-
25. Minimap and miniasm tutorial
- 25.1 Introduction
- 25.2 Data files
- 25.3 Commands
- 25.4 Details
- 25.5 Play
- 25.6 Scaling
-
26. How minimap and miniasm work
- 26.1 Details of algorithm
-
27. MUMMER
- 27.1 Quick instructions
- 27.2 Further readings
- 28. MUMMER tutorial
-
29. How MUMMER works
- 29.1 Algorithm
-
30. MUSCLE
- 30.1 Quick instructions
- 30.2 History
- 30.3 Further readings
- 31. MUSCLE tutorial
-
32. How MUSCLE works
- 32.1 Algorithm
-
33. RAPSearch2
- 33.1 Quick instructions
- 33.2 History
- 33.3 Further readings
- 34. RAPSearch2 tutorials
-
35. How RAPSearch2 works
- 35.1 Details of algorithm
- 35.2 Details of code
-
36. Samtools
- 36.1 History
- 37. Samtools tutorials
-
38. How samtools works
- 38.1 Details of algorithm
- 38.2 Details of code
-
39. SPAdes
- 39.1 Quick instructions
- 39.2 History
- 39.3 How to run
- 39.4 Features of SPAdes
- 39.5 Further readings
- 40. SPAdes tutorial
-
41. How SPAdes works
- 41.1 Details of algorithm
-
42. Trinity
- 42.1 How to run
- 42.2 History
- 42.3 Further readings
- 43. Trinity tutorial
-
44. How Trinity works
- 44.1 Details of algorithm
- 44.2 Details of code
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