mtGenome genbank file => RAxML files

 
1 May. 2021. Jun Inoue
I found some errors in this code (11 May 2021).
Overview
reconstruct_mtGenomeTree.tar.gz for protein coding genes (May 2021).

Installing Dependencies

Python3, GenBankStrip.pl, RAxML, Mafft, trimAl v1.2.

 

000 Collection of genbank files
Batch Entrez

000 GenBankStrip.pl
sh 000command.sh

010translation.pl
perl 010translation.pl
015mafft.pl
perl 015mafft.pl
020gapAddCDNA.pl
perl 020gapAddCDNA.pl
030trimal.pl
perl 030trimal.pl
040trimal_cDNA.pl
perl 040trimal_cDNA.pl
050concatenateSequence.pl

perl 050concatenateSequence.pl

060separateCodon.pl
perl 060separateCodon.pl
070make_raxmlInfile.pl
perl 070make_raxmlInfile.pl
raxml12.sh
sh raxml12.sh