EZcodon

EZcodon helps users to calculate:

1. Aminoacid frequencies over the complete submitted mitogenomes as well as for the Heavy (N) and/or Light (J) strand genes separately;
2. The RSCU (Relative Synonym Codon Usage) over the complete submitted mitogenomes as well as for the Heavy (N) and/or Light (J) strand genes separately;

Use it according to the following instructions:

1. Prepare a folder of fasta Protein Coding Genes files for each strand. If you want to input only one strand genes, then just prepare one corresponding folder. Each fasta file must be renamed as the gene name you want to analyse and contain one or more sequnces. Please check that taxa are named consistently across fasta files (i.e. if one taxon is named Drosophila in the cox1.fas file, it has to be named Drosophila in all gene files for sequences to be correctly concatenated).
2. Each of the two folders (one folder in case you submit only one strand genes) will contain the J oriented and the N oriented genes, respectively. Please name the two folders as 'J' and 'N'. Then, compress (.zip, .rar, .tar, .gz, .7z) them as a single archive with the name you desire.
3. Choose the Genetic Code for the analysis (a list of of available codes as well as some additional information can be found here.
4. Upload the files by clicking the Upload link button.
5. The output will generate a .csv tabs and .pdf graphic outputs.

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Example of the input file preparation



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Download an input example
Download an output example

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Job name*

Select the compressed archive with PCGs (separated by strand) in fasta format
Select the genetic code to use 2. The Vertebrate Mitochondrial Code 4. The Mold, Protozoan, and Coelenterate Mitochondrial Code 5. The Invertebrate Mitochondrial Code 9. The Echinoderm and Flatworm Mitochondrial Code 11. The Bacterial, Archaeal and Plant Plastid Code 13. The Ascidian Mitochondrial Code 14. The Alternative Flatworm Mitochondrial Code 21. Trematode Mitochondrial Code 24. Rhabdopleuridae Mitochondrial Code 33. Cephalodiscidae Mitochondrial UAA-Tyr Code
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*Useful to organize your processed jobs. If not provided, a random ID will be created.