choose to align the sequences by checking the “Align sequences”
checkbox (use the MAFFT as the aligner). The export of aligned
data is more time-consuming than the export of unaligned data and
is restricted for exporting 200 isolates only.
3.3 Data Analyses
3.3.1 General Overview
An easy way to get a general overview of all or selected data present
in BIGSdb is to use the breakdown option plug-ins. For example,
when you want to know the prevalence of different Leptospira
species in different geographical areas, you can click the “Two
field breakdown” link on the main contents page. This plug-in
exports a table breaking down one field against another (the breakdown of “species” by “country”) (Fig. 1) (see Note 6).
3.3.2 Interactive Tree
of Life (iTOL)
The iTOL [8] plug-in incorporated to BIGSdb enables generation
and visualization of phylogenetic trees calculated from concatenated sequence alignments of core genes (n ¼ 545) using the
neighbor-joining clustering method. It can be assessed from the
contents page or following the query by clicking the “iTOL” link.
Since this analysis requires the preassembly of the data, it is possible
to export only 200 isolates or less. The simple neighbor-joining
method produces unrooted trees, but it does not assume a constant
rate of evolution across lineages [10]. In contrast, the maximum
likelihood method uses a more complex evolution model and is
known to be stronger than the neighbor-joining method for reconstructing sequence histories [11]. In general, iTOL plug-ins which
generate the phylogenetic tree based on neighbor-joining method
are good enough for an initial overview of the phylogeny; however,
Fig. 1 The prevalence of Leptospira species around the globe. The data were generated using the “Two field
breakdown” option in the BIGSdb contents page (first of July, 2019)
14
Linda Grillova ´ and Mathieu Picardeau
checkbox (use the MAFFT as the aligner). The export of aligned
data is more time-consuming than the export of unaligned data and
is restricted for exporting 200 isolates only.
3.3 Data Analyses
3.3.1 General Overview
An easy way to get a general overview of all or selected data present
in BIGSdb is to use the breakdown option plug-ins. For example,
when you want to know the prevalence of different Leptospira
species in different geographical areas, you can click the “Two
field breakdown” link on the main contents page. This plug-in
exports a table breaking down one field against another (the breakdown of “species” by “country”) (Fig. 1) (see Note 6).
3.3.2 Interactive Tree
of Life (iTOL)
The iTOL [8] plug-in incorporated to BIGSdb enables generation
and visualization of phylogenetic trees calculated from concatenated sequence alignments of core genes (n ¼ 545) using the
neighbor-joining clustering method. It can be assessed from the
contents page or following the query by clicking the “iTOL” link.
Since this analysis requires the preassembly of the data, it is possible
to export only 200 isolates or less. The simple neighbor-joining
method produces unrooted trees, but it does not assume a constant
rate of evolution across lineages [10]. In contrast, the maximum
likelihood method uses a more complex evolution model and is
known to be stronger than the neighbor-joining method for reconstructing sequence histories [11]. In general, iTOL plug-ins which
generate the phylogenetic tree based on neighbor-joining method
are good enough for an initial overview of the phylogeny; however,
Fig. 1 The prevalence of Leptospira species around the globe. The data were generated using the “Two field
breakdown” option in the BIGSdb contents page (first of July, 2019)
14
Linda Grillova ´ and Mathieu Picardeau