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phylogeny_protocol [2021/09/20 12:27] – 134.190.232.139phylogeny_protocol [2021/09/29 12:53] (current) – 134.190.232.139
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 As mentioned in the very beginning, if your interested gene name OR ID has nothing to do with NCBI and you need the Fasta sequence. There is a simple way to do this via a custom script As mentioned in the very beginning, if your interested gene name OR ID has nothing to do with NCBI and you need the Fasta sequence. There is a simple way to do this via a custom script
-__index_header_to_seq.py__ (https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_bl ast_plus/blastxml_to_tabular.py)+__index_header_to_seq.py__ (https://github.com/zx0223winner/NoBadWordsCombiner/blob/main/Tutorial/index_header_to_seq.py)
  
 <code> <code>
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-Clustal Omega 1.2.3 (http://www.clustal.org/omega/) is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments. The usage is very straightforward:+Clustal Omega 1.2.3 (http://www.clustal.org/omega/) is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments. The usage is very straightforward: 
  
 <code> <code>
 +#For ubuntu system, simply run this to install
 +sudo apt install clustalo 
 +</code>
 +
 +<code>
 +
 ./omega_clustalo-1.2.3 -i input_file.fa -o aligned_file.fa ./omega_clustalo-1.2.3 -i input_file.fa -o aligned_file.fa
 </code> </code>
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 <code> <code>
 #!/bin/bash #!/bin/bash
-for i in $XXX+for i in *.txt
 do do
   perl pal2nal.pl amino_acid.fa nucleotide.fa -out paml.file -nogap > folder/$i   perl pal2nal.pl amino_acid.fa nucleotide.fa -out paml.file -nogap > folder/$i
phylogeny_protocol.1632151635.txt.gz · Last modified: by 134.190.232.139