Abstract:
UNLABELLED:Next-generation sequencing data can be mapped to a reference genome to identify single-nucleotide polymorphisms/variations (SNPs/SNVs; called SNPs hereafter). In theory, SNPs can be compared across several samples and the differences can be used to create phylogenetic trees depicting relatedness among the samples. However, in practice this is difficult because currently there is no stand-alone tool that takes SNP data directly as input and produces phylogenetic trees. In response to this need, PhyloSNP application was created with two analysis methods 1) a quantitative method that creates the presence/absence matrix which can be directly used to generate phylogenetic trees or creates a tree from a shrunk genome alignment (includes additional bases surrounding the SNP position) and 2) a qualitative method that clusters samples based on the frequency of different bases found at a particular position. The algorithms were used to generate trees from Poliovirus, Burkholderia and human cancer genomics NGS datasets. AVAILABILITY:PhyloSNP is freely available for download at http://hive.biochemistry.gwu.edu/dna.cgi?cmd=phylosnp.
journal_name
Genomicsjournal_title
Genomicsauthors
Faison WJ,Rostovtsev A,Castro-Nallar E,Crandall KA,Chumakov K,Simonyan V,Mazumder Rdoi
10.1016/j.ygeno.2014.06.001subject
Has Abstractpub_date
2014-07-01 00:00:00pages
1-7issue
1eissn
0888-7543issn
1089-8646pii
S0888-7543(14)00094-9journal_volume
104pub_type
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