Computational protocol: Lineage-independent retrotransposition of UTP14 associated with male fertility has occurred multiple times throughout mammalian evolution

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Protocol publication

[…] All genomic data were obtained from the ENSEMBL genome database [] (release 85—July 2016). UTP14 retrogenes were identified by using the ENSEMBL BLAST search facility with Human UTP14A as the reference sequence. Because the coding sequence of UTP14 retrogenes is intronless, they could be readily identified in all genomes and were translated into a peptide sequence using EMBOSS Sixpack ( Multi-sequence alignments were done using either Clustal Omega or T-Coffee, which are available on the EMBL-EBI website ( Alignments were manually checked for correct amino acid positioning at gaps. Anomalies were corrected and statistics recalculated as required. Maximum-likelihood phylogenetic trees were generated using software available at the website []. The options used to generate phylogenetic trees were: initial sequence alignment—muscle; alignment curation—Gblock; phylogeny—PhyML; tree rendering—TreeDyn. […]

Pipeline specifications

Software tools EMBOSS, Clustal Omega, T-Coffee, Gblocks, PhyML, TreeDyn
Application Phylogenetics
Organisms Homo sapiens