bagpipe Files

CITATION: 
Papadopoulou, A., Chesters, D., Coronado, I., De la Cadena, G., Cardoso, A., 
Reyes, J. C., Maes, J.-M., Rueda, R. M. and G¨®mez-Zurita, J. (2014), 
Automated DNA-based plant identification for large-scale biodiversity assessment. 
Molecular Ecology Resources. doi: 10.1111/1755-0998.12256


LICENSE INFORMATION: 
BAGpipe, pipeline for DNA sequence based identification of plants 
Copyright (C) 2013 Douglas Chesters and Anna Papadopoulou 
This program is free software: you can redistribute it and/or modify 
it under the terms of the GNU General Public License as published by 
the Free Software Foundation, either version 3 of the License, or 
(at your option) any later version. 

This program is distributed in the hope that it will be useful, 
but WITHOUT ANY WARRANTY; without even the implied warranty of 
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 
GNU General Public License for more details. 

You should have received a copy of the GNU General Public License 
along with this program. If not, see <http://www.gnu.org/licenses/>. 


CHANGELOG: 
03Dec2013: v1.01
22Sep2014: bagpipe_phylo.pl made available. 
           a standalone script developed from the phylogeny taxonomy assignment
           routine of BAGpipe.
           instructions for bagpipe_phylo are within the script, 
           just open with a text editor.
           and some description in:
           Chesters, Zheng, Zhu.
           A DNA Barcoding system integrating multi-gene sequence data


INSTALATION AND OPERATING INSTRUCTIONS: 
see file BAGpipeManual.docx 


FILE MANIFEST: single_linkage_1.02.pl 
create_fasta_database_from_genbank_flatfiles.pl 
parse_taxon_from_fastafile.pl 
usearch_blastout_to_tabular.pl 
dereplicate.pl 
process_distance_results.pl 
blast_query_clusters.pl 
parse_hits.pl 
concatenate_v2.pl 
format_conversion.pl 
midpoint_root.pl 
parse_clades.pl 
format_newick_IDs.pl 
parse_ncbi_tax_database.pl 
2xread 


DEPENDENCIES: 
makeblastdb 
blastn 
blastdbcmd 
usearch 
emboss 
mafft 
raxmlHPC 


OBTAIN LATEST VERSION FROM: 
https://sourceforge.net/users/dchesters 
or 
http://www.ibe.upf-csic.es/SOFT/Softwareanddata.html 


CONTACT US: 
Anna Papadopoulou, a.papadopoulou05@alumni.imperial.ac.uk 
Bugs, feature requests, Douglas Chesters, dc0357548934@live.co.uk