2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2018

Huan Fan, Anthony R. Ives, Yann Surget-Groba, Charles H. Cannon. An assembly and alignment-free method of phylogeny reconstruction fromnext-generation sequencing data. BMC genomics, 16:522. 2015.

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Download from publisher: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1647-5 PubMed

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BACKGROUND: Next-generation sequencing technologies are rapidly generating
whole-genome datasets for an increasing number of organisms. However,
phylogenetic reconstruction of genomic data remains difficult because de novo
assembly for non-model genomes and multi-genome alignment are challenging.
RESULTS: To greatly simplify the analysis, we present an Assembly and
Alignment-Free (AAF) method ( https://sourceforge.net/projects/aaf-phylogeny )
that constructs phylogenies directly from unassembled genome sequence data,
bypassing both genome assembly and alignment. Using mathematical calculations,
models of sequence evolution, and simulated sequencing of published genomes, we
address both evolutionary and sampling issues caused by direct reconstruction,
including homoplasy, sequencing errors, and incomplete sequencing coverage. From 
these results, we calculate the statistical properties of the pairwise distances 
between genomes, allowing us to optimize parameter selection and perform
bootstrapping. As a test case with real data, we successfully reconstructed the
phylogeny of 12 mammals using raw sequencing reads. We also applied AAF to 21
tropical tree genome datasets with low coverage to demonstrate its effectiveness 
on non-model organisms. CONCLUSION: Our AAF method opens up phylogenomics for
species without an appropriate reference genome or high sequence coverage, and
rapidly creates a phylogenetic framework for further analysis of genome structure
and diversity among non-model organisms.