Author image Zhenguo Zhang
and 1 contributors

Changes for version 1.04

  • 1. Update Tutorial.pod by correcting format errors and reword sentences. 2. Change program names as follows: build_cai_param.pl -> cai_codon.pl build_tai_param.pl -> tai_codon.pl calculate_CUB.pl -> cub_seq.pl The new names reflect the functions of the programs better. 3. Add a new program tabulate_codons.pl to count codons in sequence files. 4. Add one more method 'all_codons' to the module Bio::CUA::CodonTable. 5. Update help documentation.

Documentation

a program to calculate CAI for each codon
a program to calculate sequence codon usage bias metrics and other sequence parameters.
a program to output codons in a sequence file as a table
a program to calculate tAI of each codon
A tutorial on using the programs of Bio-CUA

Modules

Codon Usage Analyzer.
This is the parent class for all classs processing codon usage bias (CUB).
A module to calculate codon usage bias (CUB) metrics at codon level and other parameters
A module to calculate codon usage bias (CUB) indice for protein-coding sequences
A package processing genetic codon table
a module processing sequence object
a package to parse sequence file if module Bio::SeqIO is unavailable in the system.
a class to summarize features of sequences.