Lazarus of Bethany was brought back to life four days after his death, as described int he Gospel of John.
Lazarus is also the name of the Thornton lab program for ancestral gene reconstruction. This R package provides context and tools to help use Lazarus. Including, automatically building trees form sets of sequences.
- install required software and make sure it's on your path
- blast+
- clustalo
- readseq
- phyml
-
From within R:
install.packages("devtools") devtools::install_github("momeara/Bethany")
- Use http://www.ebi.ac.uk/Tools/hmmer to retrieve a fasta file. For PhyML, aim to get ~ 100 sequences or less.
- Run pipeline
sequences_to_trees(
sequences = <path/to/sequences.fa.gz>,
output_path = <prot_dir/data>,
run_id = <query_tool_seqdb>,
user_agent("httr <[email protected]>")) # for retrieving info from uniprot
This will produce a directory
prod_dir/data/<run_id>_YYMMDD/
<sequences.fa.gz>
# input fasta sequences
run.sh
# bash commands to re-run analysis
name_map.xlsx
# mapping between input, phylip and tree names, along with
# the sequences an and information about each sequence
# retrieved form Uniprot
clustalo_input.fasta
# input sequecences in fasta format with phylip names for clustal Omega
clustalo_output.phylip3.2
# multiple sequence alignment with phylip names in phylip3.2 format
phyml_input.phylip
# multiple sequence alignment in phylip4 format (phylip names)
phyml_input.phylip_phyml_stats_<run_id>.txt
# output log of running phyml
phyml_input.phylip_phyml_tree_<run_id>.txt
# tree generate as output from phyml (phylip names)
<run_id>.newick
# tree with informative names