Florent Angly > Bio-Community-0.001003 > bc_measure_distance


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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.







-wa <weight_assign> | -weight_assign <weight_assign>





-op <output_prefix> | -output_prefix <output_prefix>

Path and prefix for the output files. Default: output_prefix.default

-dt <dist_type> | -dist_type <dist_type>

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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  bioperl-l@bioperl.org                  - General discussion


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AUTHOR - Florent Angly ^

Email florent.angly@gmail.com

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