Computational protocol: Single colony genetic analysis of epilithic stream algae of the genus Chamaesiphon spp

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Protocol publication

[…] Sequences were aligned and conserved motifs were analyzed according to . While the 16S rDNA comprised 1149–1176 bp until the highly conserved motif D1 (), the ITS region was located between the highly conserved motif D1 and the less conserved motif D5 resulting in 608–681 bp. The sequence similarity was calculated using the PHYLIP package (version 3.69, ). All obtained 16S rDNA sequences (1149–1176 bp) were included in a phylogenetic tree constructed from previously described cyanobacterial taxa comprising all major lineages of the phylum () as well as clades found related to Chamaesiphon more recently (; ). In total, 150 non-redundant sequences obtained from strains were downloaded from the Ribosomal Database Project (RDP), (). The 16S rDNA phylogenetic tree was constructed by maximum likelihood method using the program RAxML 8.0.26 (), executing 1000 rapid bootstrap inferences and thereafter a thorough ML search. Likelihood of the final tree was evaluated and optimized using a Gamma substitution matrix (GTR). […]

Pipeline specifications

Software tools PHYLIP, RAxML
Application Phylogenetics
Chemicals Nucleotides