Question: Complete phylogenetic trees?
0
gravatar for gtrwst9
4 months ago by
gtrwst90
gtrwst90 wrote:

Hello, where can I get trees with distance information of whole classes or kingdoms like bacteria? Someone must have done this already for the known genomes. Please note, distances must be included, else it would just be a taxonomic tree.

ADD COMMENTlink modified 4 months ago • written 4 months ago by gtrwst90
1

You could look at ITOL: https://itol.embl.de/

ADD REPLYlink written 4 months ago by jrj.healey13k
0
gravatar for pltbiotech_tkarthi
4 months ago by
CIMMYT, Mexico
pltbiotech_tkarthi170 wrote:

You can predict the orthologs of protein/gene of interest from different kingdom/phyla using SMART: http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1 or http://smart.embl-heidelberg.de/smart/set_mode.cgi?GENOMIC=1 and generate the lifetree from different kingdom/phylum using ITOL. But, ITOL may not provide genetic distance, in that case, you have to use MEGA https://www.megasoftware.net/ or any other phylogenetic softwares to calculate genetic distance.

ADD COMMENTlink modified 4 months ago • written 4 months ago by pltbiotech_tkarthi170

Thanks both. Acually ITOL provides complete trees in newick, nexus and phyloxml format so, presumably, also the distances. But their example tree has only a few hundred nodes.

ADD REPLYlink modified 4 months ago • written 4 months ago by gtrwst90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1494 users visited in the last hour