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--- phylogeny_protocol [2021/09/03 16:05] – 134.190.232.139
+++ phylogeny_protocol [2021/09/29 12:53] (current) – 134.190.232.139
@@ Line 20: / Line 20: @@
 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/zx0223winner/HSDatabase/blob/master/index_header_to_seq.py)
+__index_header_to_seq.py__ (https://github.com/zx0223winner/NoBadWordsCombiner/blob/main/Tutorial/index_header_to_seq.py)
 <code>
@@ Line 45: / Line 45: @@
 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>
+#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
 </code>
@@ Line 77: / Line 83: @@
 Software requirements:
-  - PAML package (codeml)
+  - PAML package
   - pal2nal
-  - Clustal Omega 1.2.3
+  - Clustal Omega
-  - trimAl v1.2
+  - FastTree
-  - FastTree 2.1
+The calculation of synonymous (dS) and non-synonymous (dN) substitution rates is important to infer the evolutionary driving force: positive selection (dN/dS>1), neutral selection (dN/dS=1) and negative/purifying selection (dN/dS<1).
-http://abacus.gene.ucl.ac.uk/software/paml.html
-http://www.bork.embl.de/pal2nal/
+PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. http://abacus.gene.ucl.ac.uk/software/paml.html
-<code>
+PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment.http://www.bork.embl.de/pal2nal/
+This is an example of batch script when dealing with dN/dS among thousands genes.
+<code>
+#!/bin/bash
+for i in *.txt
+do
+  perl pal2nal.pl amino_acid.fa nucleotide.fa -out paml.file -nogap > folder/$i
+done
 </code>
+Shell script: codeml and configure file: codeml.ctl
 Note: Please refer to the latest version of software for the most updated information.
-{{:22-you-got-this-meme-5.jpg?nolink&200|}}
 <Last updated by Xi Zhang on Sep 3rd,2021>