PhyloProfile

Choose type of x-axis:

taxa genes

Auto update plot

Retain gene order

Width (px)

Auto sizing

Height (px)

Max co-orthologs

Choose type of x-axis:

taxa genes

Width (px)

Auto sizing

Height (px)

PhyloProfile v1.18.0

Input & settings
Main profile
Customized profile
Function
Export data
Help
- Wiki
- About

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

Order seed IDs

Color configuration:

Other optional input:

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 taxa

automatically by user defined tree by a sorted list

Display all input taxa

Select gene to highlight:

Browse...

Select (super)taxon to highlight:

Highlight genes by categories

Highlight duplicated ortholog IDs

Download profile

Select sequence(s) of interest:

Browse...

Select (super)taxon/(super)taxa of interest:

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

Download profile

Profiles clustering

Cluster method:

Width (px)

Height (px)

Apply clustering to profile plot

Add selected genes to Customized profile

Download plot

Download distance matrix Download gene list

Distribution analysis

Select data

Label size

Width (px)

Download plot

Gene age estimation

Appearance

Add selected genes to Customized profile

Download plot

Download gene list

Core gene identification

Core taxa coverage

Download gene list

Add core genes to Customized profile

Group comparison

Use common ancestor

Select in-group by supertaxon

Upload sequence(s) / In-group taxa

Compare using:

Significance level:

Add candidate gene(s) to Customized profile

Download plot

Filter gain/loss features

Number of intances per protein (IPP) cutoff

Delta IPP / Sum IPP cutoff

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

Download filtered data

Download FASTA sequences

Download data as PhyloProfile input format

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

Download customized data

Download FASTA sequences

Download data as PhyloProfile input format

Export plot settings

as:

a list

an Rscript

Output dir:

File name:

Get OMA data

Select type of OMA orthologs:

Save data
This windows will close automatically when eveything is done!

Add new taxa

Use this form to add taxon that does not exist in NCBI taxonomy database (or alternatively you can manually prepare the PhyloProfile/data/newTaxa.txt file with the following description for each field).

NOTE: ID and name of new taxon must be different from any existing NCBI taxa.

ID (must be a number and greater than 999999005, e.g. 999999901)

Name (e.g. Saccharomyces cerevisiae strain ABC)

Rank (e.g. strain, species, order, etc.)

Parent ID (NCBI taxonomy ID of the next higher rank, e.g. 4932 (S.cerevisiae species))

Or upload file contains IDs for new taxa

Browse...

Taxonomy file for new taxa has to be a tab-delimited text file and has the following header (please follow the rule above):

ncbiID fullName rank parentID

Get taxonomy info

Fetching Missing Taxonomy Information and Post-processing.

This windows will close automatically when eveything is done. Please wait...

PLEASE RELOAD THIS TOOL WHEN FINISHED!!!

Detailed plot

Height (px)

Text size (px)

Hide taxa that have no ortholog (NAs)

Apply filters

Download plot

Sequence:

Domain architecture

Plot height(px)

Plot width(px)

Title size(px)

X-axis size(px)

Show

Exclude feature type(s)

Download plot

LINKS TO ONLINE DATABASE

Disclaimer: External links are automatically generated and may point to a wrong target (see FAQ)

Domain architecture

Plot height(px)

Plot width(px)

Title size(px)

X-axis size(px)

Show

Exclude feature type(s)

Download plot

LINKS TO ONLINE DATABASE

Disclaimer: External links are automatically generated and may point to a wrong target (see FAQ)

Set colors for profile

Low variable 1 (dot)

Mid variable 1 (dot)

High variable 1 (dot)

Mitpoint varriable 1

Low variable 2 (background)

Mid variable 2 (background)

High variable 2 (background)

Mitpoint varriable 2

Color for inparalogs

FASTA upload

Choose location for:

Browse...

Main FULL path:

Directory format:

File extension:

ID format:

Upload gene categories

Browse...

Sequence ID format

ID format:

Separator:

Please note! Only these ID formats are accepted!

Plot appearance configuration

X-axis label size (px)

Y-axis label size (px)

Legend label size (px)

Legend position:

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]

Plot appearance configuration

X-axis label size (px)

Y-axis label size (px)

Legend label size (px)

Legend position:

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]

Plot appearance configuration

Width zoom (*600px)

Height zoom (*150px)

Text size zoom

Plot appearance configuration

X-axis label size (px)

Y-axis label size (px)

Title size (px)

Legend label size (px)

Options for variable plot only:

Width (px)

Height (px)

Legend position:

Show mean/median point:

Options for feature plot only:

Width (px)

Height (px)

Flip coordinates

Yes No

Angle of the X-axis label

Names of in-group and out-group taxa:

Select taxon/taxa of interest

Apply to main profile

Select taxon/taxa of interest

Apply to customized profile

Select taxon/taxa of interest

Apply

Select taxon/taxa of interest

Apply

Upload files for group comparison

Sequence(s) that need to be compared

Please use the same sequence IDs as being shown in the phylogenetic profiles!

Browse...

In-group and out-group taxa

Please upload an tab-delimited ID list of in-group and out-group taxa. The ID must follow the format " ncbi12345". Example:

ncbi12345 in-group

ncbi24242 in-group

ncbi33333 out-group

Browse...

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

Color configuration:

Other optional input:

Taxonomy DB location:

Seed (super)taxon:

Select taxonomy rank:

Choose (super)taxon of interest:

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

Export plot settings

Get OMA data

Add new taxa

Get taxonomy info

Detailed plot

Sequence:

Links:

Domain architecture

LINKS TO ONLINE DATABASE

Domain architecture

LINKS TO ONLINE DATABASE

Set colors for profile

FASTA upload

Upload gene categories

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: