PhyloProfile

Choose type of x-axis:

taxa genes

Display genes using:

Gene IDs Gene names

Retain gene order

Width (px)

Auto sizing

Choose type of x-axis:

taxa genes

Width (px)

Auto sizing

Main input:

RELOAD THIS TOOL TO UPLOAD A NEW INPUT FILE!!!

Use online demo data:

Aggregate by:

Relationship:

Aggregate by:

Relationship:

Additional annotation input:

from file from folder

New taxa were found:

Download ID list

Choose genes of interest:

all from file

Browse...

Show from:

...to:

Sequence source:

Seeds:

OrthoDB version

Orthologs:

OrthoDB version

Other optional input:

General configuration:

Colors

Font

Taxonomy DB location:

Default User-defined

Some new taxa have invalid IDs (either in newTaxa.txt or in the main profile input or both). IDs of non-NCBI taxa have to be greater than 999999005.

Please replace those IDs before continuing!

NCBI taxonomy information of some taxa can neither

be retrieved from NCBI (Source="ncbi") nor
be found in PhyloProfile/data/newTaxa.txt (Source="new") file

Please add taxonomy information for those unknown taxa and reload the tool to continue!

NCBI taxonomy information of some taxa can either

be retrieved from NCBI (Source="ncbi") or
be found in PhyloProfile/data/newTaxa.txt (Source="new") file

Click here to get required taxonomy information for those taxa!

Download invalid IDs

Seed (super)taxon:

Select taxonomy rank:

Choose (super)taxon of interest:

Order seed IDs

none alphabetically profile similarity user defined

Order taxa

automatically by user defined tree by a sorted list

Display all input taxa

Download profile

Show subplot settings

show hide

X-axis

taxa genes

Width (px)

Height (px)

Axis size

Legend size

Legend position:

Download subplot Download selected data

Please select subset of genes and/ or taxa for customized profile!

Download profile

Show subplot settings

show hide

X-axis

taxa genes

Width (px)

Height (px)

Axis size

Legend size

Legend position:

Download subplot Download selected data

Technique

# iter.

Apply on

Taxa Genes

using

Plot width

Plot height

Text size

Legend position:

Dot size zooming

Summarize as [Other] by

taxa genes

If frequency smaller or higher than Freq cutoff, labels will be grouped as [Other]

Freq cutoff

Plot dimensions

2D 3D

Transparent level

Random seed

Drag to select, then double click to zoom in. Double click empty space to zoom out

Click on data point to select

Download 3D plot

Download 2D plot

Download data

Apply clustering to profile plot

Add selected genes to Customized profile

Download gene list

Add core genes to Customized profile

Use common ancestor

Select in-group by supertaxon

Upload sequence(s) / In-group taxa

Significance level:

Add candidate gene(s) to Customized profile

Choose a task:

Update NCBI taxonomy DB

Reset NCBI taxonomy DB

Export taxonomy DB files

Import taxonomy DB files

Update NCBI taxonomy

Reset taxonomy data

Export current taxonomy files

Import your own taxonomy files

Download representative sequences

Select representative by

max min

NOTE: Depending on your choice in Download filtered data -> Main data, either all or only representative sequences will be downloaded!

Hide taxa that have no ortholog (NAs)

Apply filters

Merge non-overlapped features

Yes No

Display feature names

On the plot

As a legend

On the y-axis

Exclude features

Other feature options

Plot configuration

Show information

Weight

E-value

Bit-score

Linearizing architecture using

Type of feature names

Labels Texts

Label position

Above Inside Below

Feature name color

Exclude feature names of

Sort feature classes by shared features

Yes No

Plot height(px)

Plot width (px)

Title/Seq ID size (px)

Axis label size(px)

Legend font size(px)

Feature segment size (mm)

Feature ID size (mm)

Distance between plot title and the 1st feature

Color feature instances

Shared Unique All Feature type

Ignore number of instances

Merge non-overlapped features

Yes No

Display feature names

On the plot

As a legend

On the y-axis

Exclude features

Other feature options

Plot configuration

Show information

Weight

E-value

Bit-score

Linearizing architecture using

Type of feature names

Labels Texts

Label position

Above Inside Below

Feature name color

Exclude feature names of

Sort feature classes by shared features

Yes No

Plot height(px)

Plot width (px)

Title/Seq ID size (px)

Axis label size(px)

Legend font size(px)

Feature segment size (mm)

Feature ID size (mm)

Distance between plot title and the 1st feature

Color feature instances

Shared Unique All Feature type

Ignore number of instances

X-axis label size (px)

Y-axis label size (px)

Legend label size (px)

Group label size (px)

Height for group label

Angle for taxonomic group label:

Angle for x-axis label:

Zooming factor (α) for dots on profile:

dot size = (1+α)*defaultSize
defaultSize =[0:5]

X-axis label size (px)

Y-axis label size (px)

Legend label size (px)

Group label size (px)

Height for group label

Angle for taxonomic group label:

Angle for x-axis label:

Zooming factor (α) for dots on profile:

dot size = (1+α)*defaultSize
defaultSize=[0:5]

X-axis label size (px)

Y-axis label size (px)

Legend label size (px)

Options for variable plot only:

Show mean/median point:

Options for feature plot only:

Flip coordinates

Yes No

Angle of the X-axis label

Names of in-group and out-group taxa:

Main input:

Use online demo data:

Aggregate by:

Relationship:

Aggregate by:

Relationship:

Additional annotation input:

New taxa were found:

Choose genes of interest:

Show from:

...to:

Sequence source:

Seeds:

OrthoDB version

Orthologs:

OrthoDB version

Other optional input:

General configuration:

Taxonomy DB location:

Seed (super)taxon:

Select taxonomy rank:

Choose (super)taxon of interest:

Order seed IDs

Order taxa

Please select subset of genes and/ or taxa for customized profile!

Profiles clustering

Cluster method:

Distribution analysis

Gene age estimation

Core gene identification

Group comparison

Select in-group by supertaxon

Upload sequence(s) / In-group taxa

Update NCBI taxonomy

Reset taxonomy data

Export current taxonomy files

Import your own taxonomy files

Download processed data

Export plot settings

Point's info:

Main input:

Use online demo data:

Aggregate by:

Relationship:

Aggregate by:

Relationship:

Additional annotation input:

New taxa were found:

Choose genes of interest:

Show from:

...to:

Sequence source:

Seeds:

OrthoDB version

Orthologs:

OrthoDB version

Other optional input:

General configuration:

Taxonomy DB location:

Seed (super)taxon:

Select taxonomy rank:

Choose (super)taxon of interest:

Order seed IDs

Order taxa

Please select subset of genes and/ or taxa for customized profile!

Profiles clustering

Cluster method:

Distribution analysis

Gene age estimation

Core gene identification

Group comparison

Select in-group by supertaxon

Upload sequence(s) / In-group taxa

Update NCBI taxonomy

Reset taxonomy data

Export current taxonomy files

Import your own taxonomy files

Download processed data

Export plot settings

Get OMA data

Add new taxa

Get taxonomy info

Detailed plot

Sequence:

Links:

Domain architecture

Domain architecture

Set colors for profile

FASTA upload

Upload gene categories

Upload gene names

Sequence ID format

Plot appearance configuration

Plot appearance configuration

Plot appearance configuration

Plot appearance configuration

Select taxon/taxa of interest

Select taxon/taxa of interest

Select taxon/taxa of interest

Select taxon/taxa of interest

Upload files for group comparison

Sequence(s) that need to be compared

In-group and out-group taxa

Invalid taxa were found:

Point's info: