PhyloProfile

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...

Sequence source:

Seeds:

Orthologs:

Order seed IDs

Color configuration:

Other optional input:

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

Download profile

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

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!

Main input:

Use online demo data:

Aggregate by:

Relationship:

Aggregate by:

Relationship:

Additional annotation input:

New taxa were found:

Choose genes of interest:

Sequence source:

Seeds:

Orthologs:

Color configuration:

Other optional input:

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

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:

Sequence source:

Seeds:

Orthologs:

Color configuration:

Other optional input:

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

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

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: