Programs

Many of the programs required for completing the exercises in Bioinformatics for Evolutionary Biologists are either already part of any standard UNIX system, or can be installed on such a system using a package manager. The exceptions are the programs written and maintained by BH, and a few third-party programs. These are listed individually below. Alternatively, they can be downloaded as a single package from here.

Maintained By Bernhard Haubold

1. blast2dot.awk
2. bwt v. 0.3
3. cchar v. 1.13
4. clustDist v. 0.8
5. coalescent.awk
6. cutSeq v. 0.14
7. dnaDist v. 0.4
8. dotPlotFilter.awk
9. drawGenes v. 0.4
10. drawGenealogy v. 1.4
11. drawStrees v. 1.3
12. drawWrightFisher v. 1.3
13. fasta2tab.awk
14. gal, lal, oal, kerror v. 0.30
15. gd v. 0.15
16. genCode v. 0.4
17. genTree v. 0.5
18. getSeq v. 0.5
19. histogram v. 0.13
20. keywordMatcher v. 1.20
21. lzd v. 0.6
22. mtf v. 0.4
23. mutator v. 0.4
24. mum2plot.awk
25. naiveMatcher v. 0.2
26. new2view v. 0.13
27. numAl v. 0.6
28. pamLog v. 0.7
29. pamNormalize v. 0.7
30. pamPower v. 0.7
31. percentDiff.awk
32. randomizeSeq v. 0.8
33. ranDot.awk
34. ranseq v. 0.9
35. repeater v. 0.10
36. revComp v. 1.6
37. rpois.awk
38. sblast v. 0.7
39. sequencer v. 1.15
40. shuffle.awk
41. shustring v. 2.6
42. simNorm v. 0.1
43. simOrf.awk
44. testMeans v. 0.2
45. traverseTree v. 0.3
46. var v. 0.1
47. watterson v. 0.2

Third-Party

1. andi
2. blastn, blastp, psiblast
3. bwa
4. clustalw/2
5. ms
6. mummer, nucmer, show-snps
7. retree
8. samtools/tabix
9. sqlite-jdbc
10. velvet