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This article mainly introduces how to use iTOL to reflect the sample grouping information with color in the evolution tree, which has a certain reference value, and interested friends can refer to it. I hope you will gain a lot after reading this article.

Method 1: label color distinguishing sample grouping

The color of the label is used to distinguish the sample groups, and different colors represent different groups.

To set different font colors for each sample or gene name in the evolutionary tree above for grouping, you need to prepare the following configuration file, which is structured as follows:

TREE_COLORSSEPARATOR TABDATA155864 label # 6633ff bold 1.583334 label # 6633ff bold 1.5217992 label # 6633ff bold 1.5562 label # 6633ff bold 1.5...181661 label # 6633ff bold 1.5180835 label # 6633ff bold 1.5382 label # 6633ff bold 1.529461 label # 6633ff bold 1.5

The first three behaviors are in a fixed format, but do not need to be modified. After DATA, we will add the annotation information. There are a total of five columns of information, each separated by a Tab tab (set by the second line "SEPARATOR TAB"):

The first column: the names of species, samples, or genes in the evolutionary tree

Second column: set the modification type to label

Column 3: set the corresponding color for each sample

Fourth column: the font of the label, such as bold to indicate the use of bold

Column 5: modify the size of the label font (the larger the value, the larger the font).

We are set to the same color in the same group. This makes it easy to distinguish between different groups in the evolutionary tree.

Method 2: label background color to distinguish sample grouping

Similarly, the background color of the label can also be used to distinguish the grouping of samples, and different colors represent different groups.

To group each sample or gene name in the evolutionary tree above, you need to prepare the following configuration file, which is structured as follows:

TREE_COLORSSEPARATOR TABDATA155864 range # 6633ff test183334 range # 6633ff test1217992 range # 6633ff test1...181661 range # 6633ff test2180835 range # 6633ff test2382 range # 6633ff test2

The file format is similar to the previous configuration file, except that there are only four columns:

The first column: the names of species, samples, or genes in the evolutionary tree

Second column: set the modification type to range (add a color range on the branch, that is, add the background color to the whole branch, but only the label background color is displayed by default)

The third column: set the corresponding background color for each sample

Column 4: set the label of color range, which is of little use here.

Color setting of branches

In addition, the color of the branches of the evolutionary tree can be set, and the configuration file is as follows:

I149 clade # 00ccff normal 2I189 clade # FF0000 normal 2

The first column: the node ID in the evolutionary tree. ITOL assigns a Node id to each node when importing the nwk file, which can be viewed by clicking on the node of the evolutionary tree.

Second column: set the modification type to clade

The third column: set the color of the branch

Fourth column: set the line type, the solid line used here

The fifth column: set the thickness of the branch, the larger the value, the thicker the line.

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