Modified on April 6, 2022 
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This is a manual of the Perl programs, which can be used to extract and remove target taxa sequences from MIDORI databases. 
The Perl programs are prepared for each format. 

target_list.txt file will be used in all formats.  
In this "target_list.txt" file, users can list the name of taxa they want to extract and remove. 

Replace those taxa with your target. 
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Arachnida_6854
Aves_8782
Chilopoda_7540
Collembola_30001
Diplopoda_7553
Insecta_50557
Lepidosauria_8504
Mammalia_40674
Crocodylia_1294634
Testudines_8459
Bryopsida_3214
Magnoliopsida_3398
Amphibia_8292

* Note that GenBank taxonomy ID, which you see from above examples, need be added on your target to increase the specificity. 
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1. BLAST formats
Command example: 
$ perl filter_BLAST.pl -list target_list.txt -file MIDORI_BLAST.fasta
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2. MOTHUR formats
Command example: 
$ perl filter_MOTHUR.pl -list target_list.txt -fasta MIDORI_MOTHUR.fasta -taxon MIDORI_MOTHUR.taxon
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3. QIIME formats
Command example: 
perl filter_QIIME.pl -list target_list.txt -fasta MIDORI_QIIME.fasta -taxon MIDORI_QIIME.taxon 
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4. RAW formats 
Command example: 
$ perl filter_RAW.pl -list target_list.txt -file MIDORI_RAW.fasta
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5. RDP formats 
Command example: 
$ perl filter_RDP.pl -list target_list.txt -file MIDORI_RDP.fasta

Original taxonomy file can be used with your created target fasta file. 
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6. SINTAX formats 
Command example: 
$ perl filter_SINTAX.pl -list target_list.txt -file MIDORI_SINTAX.fasta
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