This repository contains some Perl scripts for phylogenetic analysis of mitochondrial genomes.

1. Step1_Get_gene_matrix.pl

   Usage: perl Step1_Get_gene_matrix.pl -i Species_name.txt -o Gene_matrix.txt

   The Species_name.txt file should contain all the file name of your selected data (Fasta format).

   Species_name.txt

   The purpose of this script is to generate the following gene matrix.

   Gene_matrix.txt

   Then, the users need to select the conserved single genes from the gene matrix, and output the conserved gene list for the next step.

   ConservedGene.txt

2. Step2_Generate_the_phylogeny_fa.pl

   Usage: perl Step2_Generate_the_phylogeny_fa.pl -g ConservedGene.txt -o Prefix

   This script will generate two main results:

   (1) One file named $prefix.phylogeny.fa in Fasta format for constructing the phylogenetic tree.

   (2) IQTREE results. The parameters for IQTREE are: iqtree -s $output.muscle.alignment.afa -m MFP -B 1000 --bnni -T AUTO

3. All the data can be found in the Example directory.