cuttlery

Codon Usage Table Tools for python

• cuttlery has several tools

Modules

cuttlery calculate-pi

This program calculates the value of little pi, also known as nucleotide diversity, of the sequences in a fasta alignment.

The most sensible way to use this program is to make one fasta alignment with your favorite fasta alignment program and to save it as a fasta alignment. Alternatively, you can make a fasta alignment and save each sequence to a separate fasta file.

Then, calculate little pi using cuttlery with

cuttlery calculate-pi --fasta_aln <fasta_aln1.fasta> <fasta_aln2.fasta> <et cetera>

The output will be printed to std out.

cuttlery codonplot

This program plots the codon usage of a collection of genes as violin plots. This style of plot more accurately reflects the biological variability in codon usage in different protein types. In addition, one can plot single or multiple genes as dots to highlight their position in the distribution of codon usage frequencies.

cuttlery dirichlet

In short, this test asks if the trinucleotide frequency of a test ORF more closely matches the trinucleotides frequencies of coding or noncoding DNA from the same species.

cuttlery heterogeneity

This program plots synonymous and nonsynonymous mutations along the length of a locus. The density of the mutations along the proteins' sequences are represented by sticks and a density plot.

cuttlery piNpiSsim

This program observes the nucleotide diversity of a protein-coding locus in a population of sequences. Using this information it generates other similar sequences with the same nucleotide diversity and geneaology as the observed sequences. However, the generated sequences have their mutation sites modeled from a randomly-chosen observed sequence at randomly chosen sites. This simulation may estimate the lower bounds of piN/piS for a neutrally evolving sequence of similar base composition and geneology as the observed population of protein-coding sequences.

Authors

Darrin T Schultz (github@conchoecia) Jordan M Eizenga (github@jeizenga)

Special thanks to Russell Corbett-Detig for conceiving of the tests programmed in cuttlery piNpiSsim and cuttlery heterogeneity. (github@russcd)