Computational protocol: Free-living and captive turtles and tortoises as carriers of new Chlamydia spp.

Similar protocols

Protocol publication

[…] Sequencing data were subjected to a BLAST search against the NCBI database to identify the most similar entries and aligned with a set of selected sequences representative for known chlamydial species. To assess the phylogenetic relationship between Chlamydia spp. and the tested samples, phylogenetic trees were constructed for 16S rRNA (1180bp) and IGS-23S rRNA (920 bp) as well as for ompA (920 bp) using Geneious Pro 8.0 software (Biomatters, New Zealand). The MrBayes method with 1,000 replicates bootstrap was applied. The general time-reversible (GTR) model of DNA substitution was chosen for analysis of the 16S rRNA gene and Hasegawa–Kishono-–Yano (HKY85) for 23S rRNA and ompA phylogeny, based on MEGA 6 calculations. An estimation of mean nucleotide distances was prepared with the MEGA 6 software package []. […]

Pipeline specifications

Software tools Geneious, MrBayes, MEGA
Application Phylogenetics
Organisms Chlamydia pneumoniae, Chlamydia pecorum