Welcome to SCORPiOs documentation!¶
SCORPiOs is a synteny-guided gene tree correction pipeline for clades that have undergone a whole-genome duplication event. SCORPiOs identifies gene trees where the whole-genome duplication is missing or incorrectly placed, based on the genomic locations of the duplicated genes across the different species. SCORPiOs then builds an optimized gene tree consistent with the known WGD event, the species tree, local synteny context, as well as gene sequence evolution.
SCORPiOs is implemented as a Snakemake pipeline. SCORPiOs takes as input either gene trees or multiple alignments, and outputs the corresponding optimized gene trees.
For more information, you can take a look at SCORPiOs publication.
SCORPiOs uses the following tools to build and test gene trees:
ProfileNJ: Noutahi et al. (2016) Efficient Gene Tree Correction Guided by Genome Evolution. PLOS ONE, 11, e0159559.
RAxML: Stamatakis (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312–1313.
PhyML: Guindon et al. (2010) New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Syst Biol, 59, 307–321.
TreeBeST: Vilella et al. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res., 19, 327–335.
CONSEL: Shimodaira and Hasegawa (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics, 17, 1246–1247.