Introduction to calculating dN/dS ratios with codeml v2
Abstrak
This is short tutorial on one way to calculate dN/dS ratios between pairs of protein-coding nucleic acid sequences using codeml in the PAML package. Code is intended for use on an Ubuntu 16.04 LTS OS, but it may work on other Unix or Unix-like systems. The programs used in this tutorial are: codeml in the PAML package. On a Ubuntu 16.04 LTS system it should be able to install this tool with "sudo apt install paml". http://abacus.gene.ucl.ac.uk/software/paml.html PAL2NAL. This is essentially a PERL script that you will want to have handy, either by putting it in the folder that you are working in or by putting it somewhere that is in your PATH. http://www.bork.embl.de/pal2nal/ clustal-omaga. You should be able to install this with "sudo apt install clustalo" This is a nice amino acid and nucleic acid alignement program. For purposes here your choice of aligner is not critical, so if you prefer MAFFT or Muscle or something else you can continue using those. http://www.clustal.org/omega/
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Frank O Aylward
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Cek di sumber asli →- Tahun Terbit
- 2018
- Bahasa
- en
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- 5×
- Sumber Database
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- DOI
- 10.17504/protocols.io.qhwdt7e
- Akses
- Open Access ✓