Pal2nal| how to run pal2nal from the command line

1.Pal2Nal What is it?

  Pal2Nal It is a protein that has been compared and its corresponding DNA（mRNA） A program for converting multiple sequences into codon alignment . Online web version available , Yes Linux The command line version under the operating system , This article introduces the command line version .

  Pal2Nal The official website of ：

http://www.bork.embl.de/pal2nal/

2.Pal2Pal Download and install

conda create -n pal2nal
conda activate pal2nal
conda install pal2nal

3. function Pal2Nal

perl pal2nal.pl pep.fas nuc.fas -output codon > ./*.fas -codontable number
# Input file , Two , They are better than each other PEP And the original CDS Sequence 
#-output  Output file format , The default is clustal
#-output + ' ' + > + ' ' + Enter the path and file name 
#-codontable  Select the appropriate codon table 
#pal2nal -h  You can see the detailed parameter information