Invertebrate phylogenetic tree on Ensembl

Question

[ammarsabir15]

I want to create a phylogenetic tree of the invertebrate species that are present on ensembl. In ensembl blast there are only few invertebrates present. I am not getting the exact pipeline to make a phylogenetic tree. How this can be achieved?

Answer 1

[Ben_Ensembl]

Hi,

Invertebrate species are represented by the Ensembl Genomes project: http://ensemblgenomes.org

The Ensembl genomes project is split into five divisions: plants, protists, fungi, non-vertebrate metazoans and bacteria.

Ensembl Genomes produces phylogenetic trees for each taxa division, e.g: http://metazoa.ensembl.org/Anopheles_gambiae/Gene/Compara_Tree?db=core;g=AGAP004707;r=2L:2358158-2431617;t=AGAP004707-RA

as well as a 'Pan-taxanomic' comparative analysis (including phylogenetic trees), which uses representative species from each of these five divisions, e.g: http://metazoa.ensembl.org/Anopheles_gambiae/Gene/Compara_Tree/pan_compara?db=core;g=AGAP004707;r=2L:2358158-2431617;t=AGAP004707-RA

As already suggested, you can use the help and documentation sections to see how these trees are calculated, if you wish to rebuild your own trees.

Best wishes

Ben Ensembl Helpdesk

Answer 2

[Jean-Karim Heriche]

Ensembl already has phylogenetic trees. See the compara database. If you want to rebuild the trees, you could use the same pipeline. It's described here.

[ammarsabir15]

What if I download the sequences for invertebrates and make a tree using tools like MEGA5 or Phylip?

[GenoMax]

Nothing preventing you from doing that. You can be selective about the sequences you want to include and make your own decisions about settings. It would not be a trivial exercise so keep that in mind.

[ammarsabir15]

@genomax thanks for your comments.