Phylogenetic tree generation

[jeffreybarrick]

Update code for making phylogenetic trees via gdtools PHYLOGENY and then generating graphics. This would be useful specifically for adding to the LTEE-Ecoli website.

https://github.com/barricklab/LTEE-Ecoli

[jeffreybarrick]

Notes from today:

• One can currently run gdtools PHYLOGENY to get a PHYLIP formatted file to analyze as an example. Given the limitations in terms of name length of PHYLIP format and not wanting to force a user to rely on dnapars for tree generation, we should output a different phylogenetic alignment format from gdtools COMPARE.
• A good place for example data is https://github.com/barricklab/LTEE-Ecoli. The GD files are in LTEE-clone-curated and the reference file is in reference. One should be able to reproduce the trees in this paper using these data:
• Some requested functionality
  • Coloring genomes and using symbols in a standardized way based on a metadata file describing treatments, populations, etc.
  • Detect and automatically re-scale long branches (such as those caused by mutators).
  • Root the tree based on an ancestral genome.

[jeffreybarrick]

One can now generate a multi-FASTA genotype file without any limitations on name length:

gdtools COMPARE -f FASTA

Recommend using this in any packages/pipelines for performing phylogenetic analyses.