Calculates the percentage of a partial BLAST result. The value produced slightly subestimates the actual advance, due to un-flushed output and trailing queries that could be processed but generate no results.
Estimates the sequencing depth of subject sequences. The values reported by this script may differ from those of BlastTab.seqdepth.pl, because this script uses the aligned length of the read while BlastTab.seqdepth.pl uses the aligned length of the subject sequence.
Estimates the average sequencing depth of subject sequences (genes or contigs) assuming a Zero-Inflated Poisson distribution (ZIP) to correct for non-covered positions. It uses the corrected method of moments estimators (CMMEs) as described by Beckett et al . Note that  has a mistake in eq. (2.4), that should be: pi-hat-MM = 1 - (X-bar / lambda-hat-MM). Also note that a more elaborated mixture distribution can arise from coverage histograms (e.g., see  for an additional correction called 'tail distribution' and mixtures involving negative binomial) so take these results cum grano salis.
 Lindner et al, Bioinformatics, 2013.
Sums the weights of all the queries hitting each subject. Often (but not necessarily) the BLAST files contain only best matches. The weights can be any number, but a common use of this Script is to add up counts (weights are integers). For example, in a BLAST of predicted genes vs some annotation source, the weights could be the number of reads recruited by each gene.
Generates a list of hits from a BLAST result concatenating the subject sequences. This can be used, e.g., to analyze BLAST results against draft genomes. This script creates two files using as prefix with extensions .rec (for the recruitment plot) and .lim (for the limits of the different sequences in ).
Calculates the quartiles of the length in a set of sequences. The Q2 is also known as the median. Q0 is the minimum length, and Q4 is the maximum length. It also calculates TOTAL, the added length of the sequences in the file, and AVG, the average length.
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.
Takes a table of OTU abundance in one or more samples and calculates the chao1 index (with 95% Confidence Interval) for each sample. To use it with Qiime OTU Tables, run it ignoring 1 left column and with header.
Estimates the log2-ratio of different amino acids in homologous sites using an AAsubs file (see BlastPairwise.AAsubs.pl). It provides the point estimation (.obs file), the bootstrap of the estimation (.boot file) and the null model based on label-permutation (.null file).