Manuals

1. ASReml user guides
2. ABYSS
3. BEDTools
4. Blat: Program Specifications and User Guide
5. Blast: program options and helps
6. Blast+ (new): User manual
7. Bowtie (Manual | Tutorial)
8. BRAT
9. Blastz: a genome sequence alignment program
10. BWA { BWA Tutorials: 1, 2 }
11. CAP3 (General helps | Assembly | Improved)
12. Carthagene
13. Cistematic
14. Clustalw: README
15. CRI-MAP (Documentation | Home Page | Tutorial)
16. ContigImage
17. e-PCR | me-PCR
18. Exonerate
19. fastPHASE (Abstract)
20. Long Horn Array DB
21. MEGAN
22. map2GO_slim
23. miranda - find miRNA sites
24. MPIblast
25. PHASE ( web, FAQ, etc.)
26. Otterlace ( Guidelines | User Manual )
27. Oases
28. Primer3: README
29. RepeatMasker
30. R
31. REPCLASS (cluster computer)
32. RepeatScout (cluster computer)
33. RHmapper
34. SamTools (tabix)
35. seqtk
36. SamTools
37. Shore
38. Sibs: README
39. SOAPdenovo
40. Tophat
41. Tophat-fusion
42. Velvet
43. WU-Blast: Topics
44. XPLCR"

Tutorials

1. BioPerl
2. Crimap (an anatomy | a tour)
3. OMIM
4. GBrowse Users Tutorial
5. GBrowse Admin Tutorial
6. GBrowse Configurations
7. DNA Sequence Analysis: GCG
8. DNA Sequence Analysis: Staden
9. Plink: Whole genome association analysis toolset

File formats

• ACE File Format
• AGP File Format
• ASN.1 Format
• BED File Format
• EMBL Seq Format
• Fasta File Format
• FASTA Seq Format
• Fastq File Format
• Genbank Seq Format
• GCG Seq Format
• GFF3 File Format (@wiki; @SO)
• GTF Format
• GFF3 New Spec
• GVF Format
• IG Seq Format
• Plain DNA seq
• SAM File Format
• VCF File Format
• IUPAC Codes

Links

• Helix@NIH