A relatively easy way would consist of: 1) fetch the sequences from all the good matches in your blast results (i.e. passing standard evalue and coverage thresholds) 2) try any of the predefined workflows in ete-build.
Those workflows take care of all necessary steps with just one command line (from building multiple sequence alignments to phylogenetic inference. Even a preliminary tree image is returned). You can fine tune the steps or switch what software is used for each task, but something as simple as this would allow you to run the same pipeline used in eggNOG and PhylomeDB phylogenetic databases (which include testing multiple aligners, trimming, model selection and maximum likelihood inference):
ete3 build -w eggnog41 -a sequences.faa -o output_tree
If interested, things can get much more complex :)
3.2 years ago by
jhc • 2.8k