Manuals

1. ASReml user guides
2. Blat: Program Specifications and User Guide
3. Blast: program options and helps
4. Blastz: a genome sequence alignment program
5. CAP3 (General helps | Assembly | Improved)
6. Carthagene
7. Clustalw: README
8. CriMap: README
9. ContigImage
10. e-PCR | me-PCR
11. Exonerate
12. fastPHASE (Abstract)
13. Long Horn Array DB
14. map2GO_slim
15. miranda - find miRNA sites
16. MPIblast
17. PHASE ( web, FAQ, etc.)
18. Primer3: README
19. RepeatMasker
20. R
21. REPCLASS (cluster computer)
22. RepeatScout (cluster computer)
23. RHmapper
24. For RNA works:
    Bowtie (Manual | Tutorial) | Cistematic | SamTools
25. Sibs: README
26. SOAPdenovo
27. WU-Blast: Topics

    Tutorials

28. BioPerl
29. Crimap (an anatomy | a tour)
30. OMIM
31. GBrowse Users Tutorial
32. GBrowse Admin Tutorial
33. GBrowse Configurations
34. DNA Sequence Analysis: GCG
35. DNA Sequence Analysis: Staden
36. Plink: Whole genome association analysis toolset

File formats:

• ACE File Format
• AGP File Format
• ASN.1 Format
• Fasta File Format
• Fastq File Format
• GFF3 File Format (wiki)
• GFF3 File Format (SO)
• NCBI Accession Format
• SAM File Format

Links:

• Helix@NIH