Computational protocol: Novel Pectate Lyase Genes of Heterodera glycines Play Key Roles in the Early Stage of Parasitism

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Protocol publication

[…] The published pectate lyase sequences were downloaded from the GenBank. The amino acid sequences without signal peptides were aligned using Muscle, alignment curation was performed withGblocks (v0.91b). The phylogeny was reconstructed from the alignment on the Phylogeny.fr platform [] based on the maximum likelihood method (PhyML program) and reliability for internal branches was assessed using the bootstrapping method (500). A default substitution model was selected assuming an estimated proportion of invariant sites (of 0.021) and 4 gamma-distributed rate categories to account for rate heterogeneity across sites. The tree rendering was performed using TreeDyn software (v1.83) and MAGE 5.0 []. […]

Pipeline specifications

Software tools Phylogeny.fr, PhyML, TreeDyn
Application Phylogenetics
Organisms Glycine max, Caenorhabditis elegans
Diseases Nematode Infections, Parasitic Diseases
Chemicals Mercury