25. Phylogenetics trees with ModestRr and bold (Version ModestR 6.5 or higher)

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Step by step tutorial:
Doing phylogenetic trees
with ModestR and BOLD

What do you need for this tutorial:
1. ModestR 6.5 or later
2. Internet connection
3. About 25 minutes

We’ll describe how to create
phylogenetic trees with ModestR and
BOLD data.
Follow the next steps!

Run ModestR DataManager program. You have to open an existing database or create a new one. To create a new
database you can see the tutorial nº 1 of ModestR tutorials : How to create a ModestR database.
You may also use this sample database that contains a taxonomy of some species of the Canidae family.
The sample database
with some species of
the Canidae family.

The first step is selecting the species we’ll want to use to create the phylogenetic tree. For this example we will select all
species of Canis genus.
To select a taxonomy
just check it in the
tree. You can check a
single species or a
whole level such as a
genus.

Then we have to obtain DNA data for those species. ModestR can currently download data from the BOLD database
(Barcode Of Life Data System) which provides sequence data and a BIN database (Barcode Index Numbers).
To download data from BOLD, just go to menu Import/DNA barcoding data/Download species DNA sequences from BOLD.

A dialog box will appear, allowing to select the data to be downloaded. You may choose to download all sequences
labeled with the species name, or only the sequences from a specific BIN for each species. If you are not familiar with
BOLD BIN’s please refer to BOLD documentation.
You have to check the option to import data to the current database. And also to select a folder where a copy of
downloaded data will be saved.
You may choose to download all sequences labeled with the
species name, or only the sequences from a specific BIN for
each species.
To select the BIN for a species you may choose the BIN that
contains most sequences sequences labeled with the species
name, or the BIN with the higher % of sequences for the
species.
Place the mouse cursor over any option to see an explanation.
Check the option to import data to the current
database.
Select a folder where a copy of downloaded data will be saved.
Click “OK” to continue

Downloading will start. Once completed, a dialog box will be displayed, where you can select opening the folder where a
copy of the downloaded data, opening the report file, or just accept (“OK”) and continue. Let’s select “Open folder”

In the folder you’ll find a copy of the downloaded data for each species in FASTA format and a CSV file that sumarizes the
data downloaded: number of samples for each species, and, if BIN downloading selected, number of BINS where it
appears, the BIN id selected for the species, etc.
Species Num.Samples Num.BINs
Higher.Sample.
Count.BIN(HSCB)
Num.species
.in.HSCB
Num.sequences
.in.HSCB
Sequences.for.
species.in.HSCB Other.BINS
Canis simens 2 0 0 0 0
Canis adustu 8 2 BOLD:ACQ1122 1 5 5 BOLD:AEE9377
Canis aureus 11 2 BOLD:ADM0647 1 3 3 BOLD:AAA1542
Canis latrans 17 1 BOLD:AAC5017 3 33 25
Canis lupus 1705 2 BOLD:AAA1542 12 1738 1414 BOLD:AAC5017
Canis mesom 5 3 BOLD:ADK6525 1 1 1 BOLD:ADW2121,BOLD:ACR0823
Canis rufus 0 0 0 0 0

If we come back to DataManager, we’ll see that now a DNA-shaped icon appears aside some of the species, indicating that
now there are sequences stored in the database for those species. Some of the species we selected don’t have this icon,
because no data was found in BOLD for them.

Now we have to select the species to build their phylogenetic tree. In this example we’ll select the whole Canis genus. It
doesn’t matter if some species of the selected species don’t have DNA data. Only species with DNA data will be used to
build the tree.
To select a taxonomy
just check it in the
tree. You can check a
single species or a
whole level such as a
genus.

Next we’ll go to menu Export/Export checked species DNA sequences/Distances and Phylo tree.

The first step is selecting a folder where all input and output data will be stored during the process. We recommend to
select an empty folder to avoid accidental overwriting.

The next step is setting how the sequence to be used for each species to build the tree will be selected, the style of label
for the tree, and the type of sequences marker to be used. Just place the mouse cursor over any option to see an
explanation.
For this example we’ll use the default settings. Click on “OK” to continue.

Once the process completed a dialog box will be displayed, where you can select opening the folder where data has been
saved, opening the resulting tree, or just accept (“OK”) and continue. Let’s select “Open folder”

Once the process completed a dialog box will be displayed, where you can select opening the folder where data has been
saved, opening the resulting tree, or just accept (“OK”) and continue. Let’s select “Open folder”. In the output folder we’ll
find the following files:
• inputseqs.fasta: the collection of sequences selected (one by
species) to build the tree,
• aligned.fasta: The result of the sequence alignment performed
before building the tree.
• generatephilotreescript.r: ModestR internally runs an R script
which uses several packages of the Bioconductor project and
others to perform the sequence alignment and phylo tree. In
this file you can find this full R script, which can be run in R or
Rstudio, provided you install the required packages.
• dist.matrix.csv: the obtained distance matrix between each
sequence.
• tree.newick: the obtained tree in Newick format.
• tree.rerooted.newick: the obtained tree once rerooted, in
Newick format.
• tree.rerooted.png: aa graph of the obtained tree once
rerooted, in png format.
• R_Messages_Log.txt and R_Output_Log.txt: the output and
the messages generated in R when running the script.

Let’s come back to Data Manager and go to menu Tools/Run Phylotree viewer.

A new window will be opened. It is a simple phylogenetic tree viewer that can display any tree in Newick format. Go to
menu File/Open Newick file and select the tree.rerooted.newick file located in the output folder seen before.

Once loaded, the tree will be displayed. This viewer allows some options such as changing branch spacing, using radial
tree, etc.

It was the Step by step tutorial:
Doing phylogenetic trees with ModestR and
BOLD
Thank you for your interest.
You can find this one and other tutorials in http://www.ipez.es/ModestR
By the ModestR team

25. Phylogenetics trees with ModestRr and bold (Version ModestR 6.5 or higher)

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