Computational protocol: Natural Variation of Heterokaryon Incompatibility Gene het-c in Podospora anserina Reveals Diversifying Selection

Similar protocols

Protocol publication

[…] Alignments of the DNA and amino acid sequences were done with ClustalW (). Phylogenetic trees were constructed using the Neighbor-Joining method with the software package MEGA4 (). Bootstrap supports, expressed as a percentage, were calculated over 1,000 replicates. Additionally, the sequences were analyzed for possible positive diversifying selection on het-c codons. To detect selection, we used the methods developed by , which are implemented in the HyPhy software (). Besides testing the het-c alleles, a set of 37 GLTP encoding genes from filamentous fungi found by a Blast search of the Fungal Genome Database held at the NCBI, including one P. anserina het-c allele, was tested for positive diversifying selection. The sequence accession numbers are listed in supplementary figure S8, Supplementary Material online. […]

Pipeline specifications

Software tools Clustal W, MEGA, HyPhy
Application Phylogenetics
Organisms Podospora anserina, Arabidopsis thaliana