Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2014 May 2;31(7):1697–1709. doi: 10.1093/molbev/msu105

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

PMC Copyright notice

Fig. 3. — Simplified ML bootstrap tree for the recoded protein-coding gene data set “cg75_degen12S” and 50% majority-rule consensus tree of 200 ML () bootstrap trees. Clades are labeled by their group label were possible. The codon usage bias and proportions at the three codon positions of the original “cg75” data set (i.e., without recoding) are presented to the right of the taxa (average values are given for summarized groups). This tree was chosen to display codon usage biases and G + C proportions because it seems to exemplify reconstruction errors induced by compositional effects. The topology of this tree somewhat correlates with composition and codon usages biases. Codon usage bias among Leu, Ser, and Arg is measured as the of the unbiased ratio between the usage of the two families of codons where the number of occurrences of codons of a family is divided by the number of possible codons in that family (2 or 4). Codon family labels: , ; , ; , ; , ; , ; and , . The codon bias representation is inspired by figure 1 of Inagaki and Roger (2006). Values above branches are BPs. Colors indicate taxonomic group (refer legend of fig. 1). *Prochlorococcus is an abbreviation of Prochlorococcus marinus (SO-6).

Inline graphic — Simplified ML bootstrap tree for the recoded protein-coding gene data set “cg75_degen12S” and 50% majority-rule consensus tree of 200 ML () bootstrap trees. Clades are labeled by their group label were possible. The codon usage bias and proportions at the three codon positions of the original “cg75” data set (i.e., without recoding) are presented to the right of the taxa (average values are given for summarized groups). This tree was chosen to display codon usage biases and G + C proportions because it seems to exemplify reconstruction errors induced by compositional effects. The topology of this tree somewhat correlates with composition and codon usages biases. Codon usage bias among Leu, Ser, and Arg is measured as the of the unbiased ratio between the usage of the two families of codons where the number of occurrences of codons of a family is divided by the number of possible codons in that family (2 or 4). Codon family labels: , ; , ; , ; , ; , ; and , . The codon bias representation is inspired by figure 1 of Inagaki and Roger (2006). Values above branches are BPs. Colors indicate taxonomic group (refer legend of fig. 1). *Prochlorococcus is an abbreviation of Prochlorococcus marinus (SO-6).