mfsizes

A simple command-line utility to calculate biological sequence (DNA or protein) sizes in a (multi) FASTA file. It gives averages, GC (or methionine) content, N50, N90, N95, number of N's, and total bases, and can also report by codon if requested.

Features

sequence sizes (DNA or protein)
GC content, in percentage (for each sequence and overall weighted average)
methionine content, in absolute number and percentage (protein only)
codon GC content (DNA only)
multi FASTA input files
reports average sequence size, total nucleotides, N50, N90, and N95
by default, report shows sequence names sorted in descending size order
report is tab-delimited text with results from one FASTA entry per line
gzip-compressed input supported

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License

GNU General Public License version 3.0 (GPLv3)

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Additional Project Details

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Perl

Related Categories

Perl Bio-Informatics Software

Registered

2011-05-20

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