Computational protocol: Gut Microbiome of the Critically Endangered New Zealand Parrot, the Kakapo (Strigops habroptilus)

Similar protocols

Protocol publication

[…] Sequences were analyzed using the Geneious software package and low-quality data from the ends of each sequence removed. Chimeras were identified with the Pintail algorithm using the Mallard software package and subsequently removed from the data set. Sequences were aligned via the SINA web aligner and imported into ARB using the SILVA 108 database . Sequence data were divided into operational taxonomic units (OTU) of 99% sequence identity using mothur and one sequence to represent each OTU per sample was used in tree construction. Sequences representing each OTU were submitted to the DDBJ/EMBL/GenBank databases under accession numbers JQ283115–Q283245, JQ302756, and JQ302757. Phylogenetic trees were constructed in ARB using the maximum likelihood method RAxML. Bootstrap values were calculated using 5000 parsimony replications. Unweighted UniFrac analyses were performed in mothur to statistically compare bacterial community composition among different sample types. […]

Pipeline specifications

Software tools Geneious, mothur, RAxML
Databases DDBJ
Application Phylogenetics
Organisms Strigops habroptilus
Chemicals Lactic Acid