BioBox: Collection of Tools for Sequence Analysis
This is a collection of programs for efficiently carrying
out routine sequence analysis tasks under the UNIX command line. Each
tool comes with its own documentation. Please drop me a line at
last_name at evolbio.mpg.de in case
you find an error in this software.
- cchar, v. 1.6:
Count characters in sequence data.
- cpg, v. 0.7:
Compute the CpG content of DNA sequences.
v. 0.11: Cut regions from molecular sequences.
v. 0.4: Generate pairs of
homologous DNA sequences.
- gd, v. 0.12: Calculate genetic
diversity (pi, S, and Tajima's D) from
aligned DNA sequences with or without sliding window.
- getSeq, v. 0.4:
Get specific sequences from a FASTA file containing multiple entries.
- ms2dna, v. 1.16: Generate
samples of homologous DNA sequences evolved under defined evolutionary scenarios by converting
the output of Richard
ms. As of
version 1.11, it can also deal with output generated by Gary Chen's
fast coalescent simulator MaCS
using the pipeline macs
[options] | msformatter | ms2dna -a.
v. 0.8: Randomize sequences.
- sequencer, v. 1.14:
Simulate shotgun sequencing with paired (as of
version 1.11) or unpaired reads and a user-defined error rate.
- simK, v. 0.4:
Simulate pair of sequences with given number of substitutions/site (K).