bc_measure_distance - Measure beta-diversity between communities
bc_measure_distance -input_files communities.generic \ -dist_type 'hellinger' \ -output_prefix community_distance
This script reads files containing biological communities and calculate how dissimilar they are (beta diversity). The output is a tab-delimited file containing the beta diversity between all pairs of communities. The columns of this file contain the name of the first community, of the second community, and their beta diversity, respectively. See Bio::Community::Meta::Beta for more details. Note that beta diversity metrics are based on relative abundances. Hence, any weight you provide will affect the results.
Input file containing the communities to manipulate. When providing communities in a format that supports only one community per file (e.g. gaas), you can provide multiple input files.
Tab-delimited files containing weights to assign to the community members.
When using a files of weights, define what to do for community members whose weight is not specified in the weight file (default: weight_assign.default):
* $num : assign to the member the arbitrary weight $num provided
* average : assign to the member the average weight in this file.
* ancestor: go up the taxonomic lineage of the member and assign to it the weight of the first ancestor that has a weight in the weights file. Fall back to the 'average' method if no taxonomic information is available for this member (for example a member with no BLAST hit).
Path and prefix for the output files. Default: output_prefix.default
The type of distance or beta-diversity metric to calculate: 1-norm, euclidean (2-norm), hellinger, infinity-norm, bray-curtis... Default: dist_type.default
Input file specifying the pairs of communities for which to calculate the beta-diversity. Each line of a file of pairs should have the name of two communities, separated by a tab. For each file of pairs, there will be a corresponding output file.
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To install Bio::Community, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Community
CPAN shell
perl -MCPAN -e shell install Bio::Community
For more information on module installation, please visit the detailed CPAN module installation guide.