README.md

In momeara/Bethany: Tools for ancestral gene reconstruction

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.

to install:

1. install required software and make sure it's on your path
2. blast+
3. clustalo
4. readseq
5. phyml

2) From within R:

install.packages("devtools")
devtools::install_github("momeara/Bethany")

usage

1. Use http://www.ebi.ac.uk/Tools/hmmer to retrieve a fasta file. For PhyML, aim to get ~ 100 sequences or less.
2. Run pipeline

sequences_to_trees(
    sequences = <path/to/sequences.fa.gz>,
    output_path = <prot_dir/data>,
    run_id = <query_tool_seqdb>,
    user_agent("httr <[e-mail]>")) # 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

momeara/Bethany documentation built on Aug. 6, 2019, 9:26 a.m.