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

Project Activity

See All Activity >

License

GNU General Public License version 3.0 (GPLv3)

Follow mfsizes

mfsizes Web Site

Other Useful Business Software

8 Monitoring Tools in One APM. Install in 5 Minutes.

Errors, performance, logs, uptime, hosts, anomalies, dashboards, and check-ins. One interface.

AppSignal works out of the box for Ruby, Elixir, Node.js, Python, and more. 30-day free trial, no credit card required.

Start Free

Rate This Project

User Reviews

Be the first to post a review of mfsizes!

Additional Project Details

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Perl

Related Categories

Perl Bio-Informatics Software

Registered

2011-05-20

Similar Business Software

MEGA

MEGA (Molecular Evolutionary Genetics Analysis) is a powerful and user-friendly software suite designed for analyzing DNA and protein sequence data from species and populations. It facilitates both automatic and manual sequence alignment, phylogenetic tree inference, and evolutionary hypothesis...

See Software
OmnibusX

In the world of biological data science, navigating vast and complex datasets can be a daunting task. Our software toolkit is designed to empower you by accelerating analysis, promoting accessibility, and providing comprehensive visualization tools to help you make sense of these intricate...

See Software
Genome Analysis Toolkit (GATK)

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. The GATK...

See Software
Geneious

Geneious Prime makes bioinformatics accessible by transforming raw data into visualizations that make sequence analysis intuitive and user-friendly. Simple sequence assembly and easy editing of contigs. Automatic annotation for gene prediction, motifs, translation, and variant calling. Genotype...

See Software
Evo 2

Evo 2 is a genomic foundation model capable of generalist prediction and design tasks across DNA, RNA, and proteins. It utilizes a frontier deep learning architecture to model biological sequences at single-nucleotide resolution, achieving near-linear scaling of compute and memory relative to...

See Software
Evo Designer

Evo Designer is an advanced tool developed by the Arc Institute, leveraging the capabilities of the Evo 2 genomic foundation model to facilitate DNA sequence generation and analysis. This platform enables users to input nucleotide sequences or specify organisms, prompting the model to generate...

See Software