Microbializer

Example data 10 E. coli dataset

Email:

A descriptive job title (optional):

Maximal permitted e-value:

Minimal percent of identity:

Minimal percent of members to be considered as a core gene:

Root the species tree according to this outgroup:

Apply bootstrap over the species tree? Yes No

A species name based on which the tree should be rooted

For example, if the genomic sequence in a file named: "Efergusonii_ATCC_35469.fna" is the desired outgroup, than "Efergusonii_ATCC_35469" should be provided. Of note, the outgroup name is CASE-SENSITIVE and thus should IDENTICAL to the corresponding genomic file name (excluding its extension), otherwise, the outgroup will be ignored and the resulted tree will be unrooted (as if no outgroup was provided).

The minimum required percent of gene members of an orthologs group that is required to be considered a core gene

For example:
(1) 100 means that for a gene to be considered core, all strains should have a member in the group.
(2) 50 means that for a gene to be considered core, at least half of the strains should have a member in the group.
(3) 0 means that every gene should be considered as a core gene.

The minimum percent of identity required for a pair of best reciprocal hits

For example:
If the cutoff is set to 80, every best reciprocal hit pair with less than 80% identity will be filtered out.

The maxmimum permitted e-value for a pair of best reciprocal hits

For example:
If the cutoff is set to 0.01, every best reciprocal hit pair with greater e-value will be filtered out.

Bootstrap procedure

If marked "Yes", 100 bootstrap iterations will be applied over the data set. In any case, no bootstrap will be applied for a data set with more than 100 genomes as bootstrap over large data, even when being parallelized into a few threads, might take hundreds of hours. If you do need to run bootstrap for larger data sets, please contact us directly and we will try to assist, per request.