RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include:

• Support for custom matrices ( without KA-Statistics ).
• Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.
• Support for cross_match-like masklevel filtering.

https://anaconda.org/bioconda/rmblast

Address of the bookmark: http://www.repeatmasker.org/RMBlast.html

he CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the system alongside any other operating system. Source codes for all programs are provided under GNU license, which makes it possible to transfer the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing the diversity within the class Negativicutes, represented by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures.

 Paper: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0060120

Address of the bookmark: http://www.cbs.dtu.dk/biotools/CMGtools/

What is Magic Wormhole?
Magic Wormhole is an open-source command-line tool that allows you to securely send files or text from one computer to another. Developed by Brian Warner, it aims to eliminate the usual hassle of file transfers: setting up SSH servers, dealing with firewall rules, cloud storage uploads, or even worrying about man-in-the-middle attacks.

Using a combination of PAKE (Password-Authenticated Key Exchange) protocols and end-to-end encryption, Magic Wormhole ensures that the only parties who can see your data are you and your recipient.

“It uses PAKE to establish a secure channel between two computers that use the same one-time code.”

How Does It Work?

One user runs a command like wormhole send file.txt.

The tool generates a human-readable, one-time code (like 7-horse-staple).

The other user types wormhole receive and enters the code.

The file is encrypted, transferred directly (or relayed if needed), and decrypted only on the recipient's side.

All of this happens over a secure channel, with no manual key exchange, configuration, or trust in a central authority.

Example Usage
# Sender
wormhole send myfile.pdf
Sending 1.4 MB file named 'myfile.pdf'
Wormhole code is: 7-horse-staple

# Receiver
wormhole receive
Please enter code: 7-horse-staple
Receiving file (1.4 MB) into: myfile.pdf

That’s it! No email attachments, no cloud storage, no FTP setups.

Why Use Magic Wormhole?
End-to-end encrypted transfers using modern cryptography.

Easy to use even for non-technical users.

Cross-platform: Works on Linux, macOS, and Windows.

No servers needed (except for a lightweight transit relay).

Works even behind NAT/firewalls.

It’s particularly ideal for:

Quickly sharing secrets or passwords.

Distributing software packages securely.

Moving files between servers or VMs.

Under the Hood
Magic Wormhole is written in Python and uses:

SPAKE2 for key exchange.

Transit relay and Mailbox server for message delivery.

Twisted framework for asynchronous networking.

The communication process is decentralized and designed to minimize the trust placed in the relay infrastructure. Even if an attacker intercepts the transit server, they cannot decrypt your data.

Installation

You can install it easily with pip:

pip install magic-wormhole

There’s also a Homebrew package for macOS users:

brew install magic-wormhole
Community and Ecosystem
Magic Wormhole is more than just a file transfer tool. It's part of a growing ecosystem that values user-centric cryptography. There are community-maintained libraries for other languages (e.g., Go, Rust), GUI frontends like wormhole-gui, and integration projects for mobile and web use.

Limitations

While Magic Wormhole is elegant and secure, it’s primarily a command-line utility and not designed for high-volume or persistent file sharing. Transfers require both sender and receiver to be online at the same time. And since it’s peer-to-peer, very large files may suffer performance issues.

Conclusion
Magic Wormhole is a breath of fresh air in the complex world of secure communication. It proves that cryptographic security doesn’t need to come with a heavy user experience cost. If you’re looking for a simple, secure, and delightful way to send files or messages, give Magic Wormhole a try.

Explore the documentation: https://magic-wormhole.readthedocs.io

https://pandoc.org/index.html

Address of the bookmark: https://pandoc.org/

• viewing files and directories;
• editing, copying and renaming files;
• and many other actions.

https://www.farmanager.com/

Basic instruction at

https://conemu.github.io/en/FarManager.html

Plugins at 

https://plugring.farmanager.com/

Address of the bookmark: https://www.farmanager.com/

http://en.wikipedia.org/wiki/Sequence_assembly 

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y

Address of the bookmark: https://sourceforge.net/projects/operasf/

Address of the bookmark: https://github.com/reubwn/hgt

To cite Mugsy, use:

Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes.Bioinformatics 2011 27(3):334-4

Address of the bookmark: http://mugsy.sourceforge.net/

https://www.nature.com/articles/nmeth.4556

Address of the bookmark: https://github.com/ryanlayer/giggle

Address of the bookmark: https://mummer4.github.io/