/paml_automation

Scripts for automating codeml

Primary LanguagePython

#paml_automation#

This set of scripts allows you to automate running codeml from PAML It adds nothing new, and is simply an automation tool.

##Program Requirements##

  1. Python2, Biopython, and docopt
  2. GNU Make and base UNIX commands

##Data Requirements##

  1. Multi-sequence alignments in FASTA format (filetype ending .fasta)
  2. A single Newick style phylogenetic tree (filetype ending .tre) with the same tip names as sequence identifiers in your FASTA file

###Usage###

  1. Clone/download this repository
  2. Place all sequence files and tree file in the root directory of the project
  • FASTA files must use the .fasta filetype
  • Tree files must use the .tre filetype
  1. Open a terminal window and cd to the project directory
  2. Type make followed by method= any of the following commands to execute the program
  • branchsites: Run Branch-Sites Test 2
  • branch: Run Branch test
  • all: Run both Branch and Branch-Sites 2 test
  • alternative: Run the alternative model of Branch-Sites Test 2
  • null: Run the null model of Branch-Sites Test 2
  • m0: Run the one-ratio model of Branch test
  • nratios: Run the n-ratio model of Branch test
  • clean: Removes any files created by make

###Completed features:###

  • Input a fasta file with any name and convert it into a phylip file suitable for use in PAML
  • Run Branch-Sites Test 1 & 2
  • Write results into a .csv file
  • Analyze results using R
  • Create a table with results

###Features to be added:###