Validation:
In order to validate the performance of RTD-based alignment-free method, 5 data sets, as listed in Table 1, were compiled by considering different factors such as,
- Variation in length of sequences
- Representation of different domains of life viz., viruses, prokaryotes and eukaryotes (Note: Classification of viruses as living or non-living is the issue of debate)
- Variation in extent of sequence similarity due to different taxonomic ranks (genotypes, species, family, class). Therefore, these data sets comprised of highly similar sequences belonging to genotypes of the same species to dissimilar sequences representing distant members of the class. The summary of data sets is given in Table 1.
- Objectives and types of various phylogeny studies such as multilocus sequence typing (MLST), which involves use of multiple genes, genotyping of isolates of the same species using single gene/genomic regions, identification of new species using complete genomes etc. apart from the study of biomolecular evolution.
Table 1: Summary of data sets used in
the study
|
Sr. no. |
Data set |
Taxon |
aOTUs |
bLength |
cLength |
dIdentity (%) |
|
1 |
MLST genes |
Genus Aeromonas |
115 |
4676-4957 |
4987 |
82.17 - 100 |
|
2 |
SH gene |
Mumps virus genotypes |
32 |
316-318 |
318 |
72.64 - 100 |
|
3 |
Mitochondrial genome |
Class Mammalia |
31 |
16338-17447 |
20317 |
61.42 - 97.78 |
|
4 |
Complete genome |
Genus Enterovirus |
113 |
6944-7458 |
8006 |
51.91 - 98.98 |
|
5 |
Complete genome |
Family Flaviviridae |
59 |
9406-12813 |
17163 |
33.40 - 90.81 |
a: number of operational taxonomic units (OTUs); b: length
variation of unaligned sequences; c: length of aligned
sequences; d: variation of percent identity in aligned
sequences. Data sets are listed in decreasing order of %
sequence identity.
Results: Phylogenetic trees
Genus Aeromonas
The MLST of the genus Aeromonas obtained using RTD-based method at k = 5.
Genotypes of Mumps virus
The phylogenetic tree of Mumps virus genotypes obtained using RTD-based method at k = 4. (adapted from Kolekar et al., 2011)
Class Mammalia
The mitochondrial genome based phylogenetic tree of species of class Mammalia obtained using RTD-based method at k = 6.
Genus Enterovirus
The complete genome based phylogenetic tree of Rhinoviruses of the genus Enterovirus obtained using RTD-based method at k = 7.
Family Flaviviridae
The phylogenetic tree obtained for the family Flaviviridae using RTD-based method at k = 1.