###MB-pipeline-DC/README.md

######Linux pipeline for metabarcoding.
######available at https://sourceforge.net/projects/metabarcode-pipe/

required software:

• usearch4.2.66_i86linux32 (http://www.drive5.com/usearch/download.html)
• raxmlHPC (newest version, also you will need version 7.2.7 if you want to use pplacer for taxonomic placement) (https://github.com/stamatak/standard-RAxML, http://sco.h-its.org/exelixis/web/software/raxml/index.html)
• mafft and clustalw for multiple sequence alignments (http://mafft.cbrc.jp/alignment/software/) (http://www.clustal.org/clustal2/#Download)
• pynast and mothur for aligning query sequences to reference alignment (http://biocore.github.io/pynast/) (http://www.mothur.org/wiki/Download_mothur)
• raxmlEPA (included in raxmlHPC package)
• pplacer (http://matsen.fhcrc.org/pplacer/)

required scripts:

• download_mamDB16S_Entrez.pl
• create_fasta_database_from_genbank_flatfiles_ccyx.pl
• create_fasta_database_from_genbank_flatfiles_Hsapiens.pl
• format_conversion.pl
• multiple_sequence_splitter.pl
• parse_taxa_overlapping_newick_and_fasta.pl
• preprocess_fasta_database.pl
• species_filter.pl

required files:

• BE_mammal_supertree.nwk (a prevously published supertree phylogeny of mammals by Bininda-Emonds)