BIBI Introduction

leBIBI IV 16S Automated ProKaryotes Phylogenylogo LBBE

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Advanced mode: Submit your query

Query Format

Format must be FASTA: >your_description
ATGCATGC... the nucleic sequence (16S, 23S will hopefully come soon)

OR #Genus_species :

for exemple #Methanothermus_sociabilis, Note that BLAST may not return all relevant sequences.

DB choice

The default DB is the "reference non redundant sequence DB" containing one sequence per species. These sequences are selected on their quality and representativity.
You cannot add a limited number of sequences in the highest interest zone of the phylogenetic tree (consider using the optimized phylogeny entry).

Parameters

The default number if sequences is 100, you may increase it up to 400

The default ALIGNER is kalign

The default trimming tool is only removing columns with more than 45% gaps

Trying to mitigate low quality positions of the query is the default
(mitigation not available if Gblocks is the trimmer)

Polytomy when nodes SH level under 0.2 is the default

Rooting by minimal variance is the default