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treehugger.pl

A pipeline to grab, label, align and trim sets of homologous proteins using a query and calculate a phylogeny
it runs along with fungison.pl using the same database

Installation

Just download the script and place it in the same folder fungison.pl and the /bin directory

Dependencies:

blast+

  sudo apt install blast+

muscle

  sudo apt install muscle

trimal

  wget https://github.com/inab/trimal/archive/refs/heads/trimAl.zip
  unzip trimAl.zip
  cd trimal-trimAl/source
  make
  sudo mv trimal /usr/bin
  cd ..
  cd ..
  rm -r trimal-trimAl
  rm trimAl.zip

iqtree

  sudo apt install iqtree

The /bin/GENOMES folder is requiered
The /bin/GENOMES.IDs file should be available

Usage

USAGE: perl treehugger.pl <OPTIONS>
OPTIONS:\n
-q FILE.query   	|QUERY FILE, [a file with .query extension}
-e 0.0000001		|E-VALUE CUTOFF, [a number]
-s 200	        	|BIT-SCORE CUTOFF [a number]
-x n or -F FORMATDB	|FORMAT THE DATABASE  ['no' is the recommeded option or 'FORMATDB']
-a yes/no		|ALIGNS THE HIT SEQUENCES, [yes/no]
-t yes/no		|TRIMS THE HIT SEQUENCES WITH MUSCLE, [yes/no]
-p yes/no		|CALCULATES A PHYLOGENETIC TREE [yes/no]

Examples:
perl treehugger.pl  -q gluc.query  -e 0.00001 -s 100 -x no -a yes -t yes -p yes
perl treehugger.pl  -q gluc.query  -e 0.00001 -s 100 -x FORMATDB -a yes -t yes -p yes