Enveomics collection

AlphaDiversity.pl

Takes a table of OTU abundance in one or more samples and calculates the Rao (Q_alpha), Rao-Jost (Q_alpha_eqv), Shannon (Hprime), and inverse Simpson (1_lambda) indices of alpha diversity for each sample.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Perl.

§ Usage

§ Arguments

Input table*

 -i in_file  Columns: samples, rows: OTUs, first column: OTU names).

Discard rows

 -r integer  Number of rows to ignore.

Discard left columns

 -c integer  Number of columns to ignore after the first column (i.e., between the first column, containing the name of the categories, and the first column of abundance values).

Discard right columns

 -C integer  Number of columns to ignore at the end of each line.

Delimiter

 -d string  Character (or string) separating columns.

Supported escaped characters are: '\t' (tabulation), and '\0' (null bit).

Headers

 -h   The first row is assumed to have the names of the samples.

Distances file

 -D in_file  A squared matrix (or bottom-left half matrix) with the distances between categories (OTUs or functions). The first column must contain the names of the categories, and it shouldn't have headers. If not set, all distances are assumed to be one.

Only used for Rao.

Skip Rao

 -R   Do not calculate Rao indices.

This significantly decreases the total running time. Note that Rao indices are highly susceptible to precision errors, and shouldn't be trusted for very big numbers.

q for qD

 -q integer  Estimate the qD index (true diversity order q).

Output file*

 out_file