Computational protocol: Evolution of pigment synthesis pathways by gene and genome duplication in fish

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Protocol publication

[…] All nucleotide sequences obtained from BLAST searches were loaded into BioEdit [], translated into proteins, and aligned using ClustalW [] as implemented in BioEdit. Alignments were carefully checked and ambiguously aligned regions were removed prior to phylogeny analyses. Identical sequences were removed.Larger draft neighbour-joining trees were obtained with MEGA3 []. Based on these trees, outgroups for final phylogenies were chosen. These were either the closest human paralog to the gene under investigation (in case of larger vertebrate gene families) or invertebrate orthologs.Final protein maximum likelihood phylogenies were computed with PHYML [,] with 100 bootstrap replicates. Models of protein evolution and parameter values were determined with ProtTest []. PAUP [] was used to obtain neighbor-joining bootstrap values of 10,000 replicates. […]

Pipeline specifications

Software tools BioEdit, Clustal W, MEGA, PhyML, ProtTest, PAUP*
Application Phylogenetics
Chemicals Guanosine Triphosphate