PhyloTools

perl scripts for
phylogenetic analyses

Contact:
   degen1@phylotools.com

Degeneracy Coding: Degen v1.4

You can apply degeneracy coding to your own aligned data sets in NEXUS, FASTA or FLAT format through this web service. We enforce an upper file size limit of 5MB (e.g., about 500 taxa with 10kbp or 50 taxa with 100kbp). If you want to degenerate larger matrices, download and run the perl script on your own machine.

Please acknowledge the use of our script/service through citation. The script and this web service are provided as a courtesy and as are - check the encoded data carefully!


DATA REQUIREMENTS:

  • NEXUS, FASTA or FLAT format (non-interleaved advisable)
  • STANDARD genetic code is default, but various other codes can be selected, too (see overview)
  • all sequences must start with a first and end with a third codon position
  • file size less than 5MB


Choose a file in NEXUS, FASTA or FLAT format to upload (5MB max.):

OR


Paste your sequences in NEXUS, FASTA or FLAT format here (5MB max.):


Choose a genetic code (STANDARD is default; see the NCBI list of genetic codes for details):
#1: The Standard Code (DEFAULT))
#2: The Vertebrate Mitochondrial Code
#3: The Yeast Mitochondrial Code
#4: The Mold / Protozoan / Coelenterate Mitochondrial Code & Mycoplasma / Spiroplasma Code
#5: The Invertebrate Mitochondrial Code
#6: The Ciliate / Dasycladacean / Hexamita Nuclear Code
#9: The Echinoderm and Flatworm Mitochondrial Code
#10: The Euplotid Nuclear Code
#11: The Bacterial / Archaeal / Plant Plastid Code
#12: The Alternative Yeast Nuclear Code
#13: The Ascidian Mitochondrial Code
#14: The Alternative Flatworm Mitochondrial Code
#S: The Standard Code - alternative encoding with Ser1 to Ser2
#Z: The Standard Code - alternative encoding with Ser2 to Ser1
#SZ: The Standard Code - alternative encoding with Ser1 and Ser2 to NNN