Computational protocol: A Complex Suite of Forces Drives Gene Traffic from Drosophila X Chromosomes

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Protocol publication

[…] Coding sequence annotations from the were used in this analysis. Three species were excluded (Drosophila simulans, Drosophila sechellia, and Drosophila persimilis) because they are very closely related to other sampled species and had their genomes sequenced to low coverage. We therefore analyzed genes in the remaining nine species (). Briefly, genes in non-D. melanogaster species were identified via a variety of methods, and the gene models were reconciled using GLEAN (; ). The GLEAN predictions, along with D. melanogaster gene models (release 4), were assigned to homologous gene families using fuzzy reciprocal Blast (FRB). The FRB gene families were then filtered for known transposable elements and aligned using MUSCLE (), as described previously (). Neighbor-Joining trees were built using these alignments, with distances calculated using the amino acid sequences of the genes. The gene trees and species trees were reconciled using NOTUNG (). […]

Pipeline specifications

Software tools MUSCLE, Notung
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Drosophila melanogaster, Drosophila pseudoobscura, Drosophila willistoni, Homo sapiens