Science and Technology Production

GitHub repository - Cydrasil: a comprehensive phylogenetic tree of cyanobacterial 16S rRNA gene sequences

Congress

Authorship:

Daniel W Roush ; Ana Giraldo Silva ; Vanessa Fernandes ; Náthali Maria Machado del Lima ; Nelson, Corey ; Sam McClintock ; VELASCO AYUSO, SERGIO ; Kevin Klicki ; Blake Dirks ; Kira Sorochkina ; Garcia-Pichel, Ferran

Date:

2018

Publishing House and Editing Place:

GitHub repository

Summary *

This is a phylogenetic tree containing 980 cyanobacterial sequences, downloaded from NCBI and used for placement of sequence variants (sOTUs) from 16s rRNA gene amplicon studies. The reference alignment was generated using SSUALIGN1 with default parameters and then masked using SSUMASK with the automatically computed alignment confidence values (posterior probabilities). A maximum-likelihood phylogenetic tree was then generated using the RAxML-HPC22 Workflow on XSEDE (8.2.1) on the CIPRES Science Gateway3. The ML + thorough bootstrap workflow was used with the following modified parameters: 1000 bootstraps (-N 1000) and the GTRGAMMA model. All other parameters were left at default values. Information provided by the agent in SIGEVA

Key Words

Phylogenetic tree16s rRNACyanobacteria